Rapid Response Group Resources

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Work</a> <a href="/sf/research-groups/" class="subtitle">Research Groups</a> <a href="https://www.czbiohub.org/rapid-response/" class="subtitle">Rapid Response</a> </div> <div class="hero__content-title"> <h1>Resources</h1> </div> </div> </div> </div> </section> <section class="primary-section--content"> <div class="container"> <div class="intro-copy"> <p>The Rapid Response Team provides pathogen genomics training and support to groups all over the world with a focus in metagenomics (mNGS) and genomic epidemiology. Here you will find protocols and training materials developed in collaboration with the Genomics and Infectious Disease teams at CZ Biohub San Francisco and the <a href="https://chanzuckerberg.com/" target="_blank" rel="noopener">Chan Zuckerberg Initiative</a>.</p> </div> <div class="row"> <div class="rail-wrap"> <button class="mobile-dropdown-icon" type="button"> <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 18 11" fill="none"> <path d="M16.5056 1.50001L8.74511 9.26052L0.984608 1.50001" stroke="white" stroke-width="2"/> </svg> </button> <div class="wrap"> <a class="is-show nav-item is-active getting-started" href="#getting-started"> <div class="icon"> <svg width="25" height="25" viewBox="0 0 25 25" fill="none" xmlns="http://www.w3.org/2000/svg"> <path d="M11.6465 23.5992C11.6465 23.5992 9.62648 22.7072 8.21448 22.1842C7.28848 21.8402 7.42048 20.2782 7.95648 19.6902C8.89631 18.7691 9.36054 17.4671 9.21548 16.1592C9.29566 15.3042 9.00566 14.4559 8.41889 13.829C7.83212 13.2021 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stroke-linejoin="round"/> <path d="M4.39648 8.09912C4.39648 7.96105 4.50841 7.84912 4.64648 7.84912" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M4.64648 8.34912C4.50841 8.34912 4.39648 8.23719 4.39648 8.09912" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M4.89648 8.09912C4.89648 8.23719 4.78456 8.34912 4.64648 8.34912" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.64648 11.8491C5.78456 11.8491 5.89648 11.961 5.89648 12.0991" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.39648 12.0991C5.39648 11.961 5.50841 11.8491 5.64648 11.8491" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.64648 12.3491C5.50841 12.3491 5.39648 12.2372 5.39648 12.0991" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.89648 12.0991C5.89648 12.2372 5.78456 12.3491 5.64648 12.3491" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M11.6465 7.84912C11.7846 7.84912 11.8965 7.96105 11.8965 8.09912" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M11.3965 8.09912C11.3965 7.96105 11.5084 7.84912 11.6465 7.84912" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M11.6465 8.34912C11.5084 8.34912 11.3965 8.23719 11.3965 8.09912" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M11.8965 8.09912C11.8965 8.23719 11.7846 8.34912 11.6465 8.34912" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M19.6465 8.34912C19.7846 8.34912 19.8965 8.46105 19.8965 8.59912" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M19.3965 8.59912C19.3965 8.46105 19.5084 8.34912 19.6465 8.34912" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M19.6465 8.84912C19.5084 8.84912 19.3965 8.73719 19.3965 8.59912" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M19.8965 8.59912C19.8965 8.73719 19.7846 8.84912 19.6465 8.84912" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.6465 10.8491C18.7846 10.8491 18.8965 10.961 18.8965 11.0991" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.3965 11.0991C18.3965 10.961 18.5084 10.8491 18.6465 10.8491" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.6465 11.3491C18.5084 11.3491 18.3965 11.2372 18.3965 11.0991" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.8965 11.0991C18.8965 11.2372 18.7846 11.3491 18.6465 11.3491" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.6465 10.8491C12.7846 10.8491 12.8965 10.961 12.8965 11.0991" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.3965 11.0991C12.3965 10.961 12.5084 10.8491 12.6465 10.8491" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.6465 11.3491C12.5084 11.3491 12.3965 11.2372 12.3965 11.0991" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.8965 11.0991C12.8965 11.2372 12.7846 11.3491 12.6465 11.3491" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> </svg> </div> <h4>Study Design</h4> </a> <a class="is-show nav-item mngs-protocols" href="#mngs-protocols"> <div class="icon"> <svg width="24" height="24" viewBox="0 0 24 24" fill="none" xmlns="http://www.w3.org/2000/svg"> <path d="M19.7599 7.39109C20.9434 7.51414 22.1394 7.37028 23.2599 6.97009" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.01696 23.2302C7.70164 21.3354 7.6416 19.2514 6.84896 17.3992C5.59439 14.367 6.29069 10.8776 8.61296 8.55915C10.3696 6.81122 12.8225 5.95145 15.286 6.22015" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.28595 17.9991C11.6614 18.1771 13.997 17.314 15.6859 15.6341C18.0081 13.3144 18.704 9.82407 17.4489 6.79114C16.6571 4.94171 16.596 2.86084 17.2779 0.96814" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M1.03296 17.2202C2.226 16.7917 3.50417 16.6545 4.76096 16.8202" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.7549 6.33716L17.9069 11.4892" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M16.97 2.06714L22.177 7.27314" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M2.12097 16.9161L7.32797 22.1231" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.77399 7.59912L16.646 14.4701" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.39093 12.7002L11.5429 17.8532" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.65198 9.72009L14.524 16.5911" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> </svg> </div> <h4>mNGS protocols</h4> </a> <a class="is-show nav-item enrichment-and-depletion" href="#enrichment-and-depletion"> <div class="icon"> <svg width="22" height="25" viewBox="0 0 22 25" fill="none" xmlns="http://www.w3.org/2000/svg"> <path d="M2.89581 13.6016V10.1016" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.89578 20.4255L6.08478 19.1025" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M16.8958 19.0135L14.8958 19.9545" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M19.8958 10.1016V13.6016" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M14.5808 4.10059L16.7128 5.10359" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.08276 5.10159L8.89576 3.77759" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M4.39578 7.92359C3.84519 8.54654 2.96663 8.7639 2.1891 8.46953C1.41156 8.17517 0.897217 7.43048 0.897217 6.59909C0.897217 5.76769 1.41156 5.023 2.1891 4.72864C2.96663 4.43428 3.84519 4.65164 4.39578 5.27459" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M4.39578 18.9236C3.84519 19.5465 2.96663 19.7639 2.1891 19.4695C1.41156 19.1752 0.897217 18.4305 0.897217 17.5991C0.897217 16.7677 1.41156 16.023 2.1891 15.7286C2.96663 15.4343 3.84519 15.6516 4.39578 16.2746" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M21.3958 7.92359C20.8452 8.54654 19.9666 8.7639 19.1891 8.46953C18.4116 8.17517 17.8972 7.43048 17.8972 6.59909C17.8972 5.76769 18.4116 5.023 19.1891 4.72864C19.9666 4.43428 20.8452 4.65164 21.3958 5.27459" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M21.3958 18.9236C20.8452 19.5465 19.9666 19.7639 19.1891 19.4695C18.4116 19.1752 17.8972 18.4305 17.8972 17.5991C17.8972 16.7677 18.4116 16.023 19.1891 15.7286C19.9666 15.4343 20.8452 15.6516 21.3958 16.2746" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M13.3958 3.92359C12.8452 4.54654 11.9666 4.7639 11.1891 4.46953C10.4116 4.17517 9.89722 3.43048 9.89722 2.59909C9.89722 1.76769 10.4116 1.023 11.1891 0.728641C11.9666 0.434278 12.8452 0.651638 13.3958 1.27459" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M13.3958 22.9236C12.8452 23.5465 11.9666 23.7639 11.1891 23.4695C10.4116 23.1752 9.89722 22.4305 9.89722 21.5991C9.89722 20.7677 10.4116 20.023 11.1891 19.7286C11.9666 19.4343 12.8452 19.6516 13.3958 20.2746" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> </svg> </div> <h4>Enrichment and depletion</h4> </a> <a class="is-show nav-item sequencing" href="#sequencing"> <div class="icon"> <svg width="25" height="24" viewBox="0 0 25 24" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M7.14648 11.5991C9.07948 11.5991 10.6465 10.0321 10.6465 8.09912C10.6465 6.16612 9.07948 4.59912 7.14648 4.59912C5.21349 4.59912 3.64648 6.16612 3.64648 8.09912C3.64648 10.0321 5.21349 11.5991 7.14648 11.5991Z" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.14648 4.59912V8.09912H10.6465" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.14648 22.0991C10.0523 20.9554 10.5769 19.5565 10.6465 18.0991" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M15.1465 22.0991C14.2407 20.9554 13.7161 19.5565 13.6465 18.0991" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M7.64551 22.0991H16.6455" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M0.646484 15.0991H23.6465" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path fill-rule="evenodd" clip-rule="evenodd" d="M0.646484 2.09912C0.646484 1.54684 1.0942 1.09912 1.64648 1.09912H22.6465C23.1988 1.09912 23.6465 1.54684 23.6465 2.09912V17.0991C23.6465 17.6514 23.1988 18.0991 22.6465 18.0991H1.64648C1.0942 18.0991 0.646484 17.6514 0.646484 17.0991V2.09912Z" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M13.6465 6.59912L15.1465 4.59912L18.1465 7.09912L20.6465 4.09912" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M19.6465 12.0991V10.5991" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M17.6465 12.0991V10.0991" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M15.6465 12.0991V9.09912" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M13.6465 12.0991V10.5991" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> </svg> </div> <h4>Sequencing</h4> </a> <a class="is-show nav-item quality-control" href="#quality-control"> <div class="icon"> <svg width="26" height="26" viewBox="0 0 26 26" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M13.1465 25.2866C19.8775 25.2866 25.334 19.8301 25.334 13.0991C25.334 6.36815 19.8775 0.911621 13.1465 0.911621C6.41551 0.911621 0.958984 6.36815 0.958984 13.0991C0.958984 19.8301 6.41551 25.2866 13.1465 25.2866Z" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.578 9.55481L12.6772 17.4239C12.4117 17.777 12.0062 17.9976 11.5656 18.0288C11.1249 18.0599 10.6924 17.8986 10.3799 17.5864L7.33301 14.5395" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> </svg> </div> <h4>Quality Control</h4> </a> <a class="is-show nav-item analysis" href="#analysis"> <div class="icon"> <svg width="20" height="20" viewBox="0 0 20 20" fill="none" xmlns="http://www.w3.org/2000/svg"> <path d="M3.28784 0.514366C3.5863 0.511798 3.88235 0.568045 4.15908 0.679895C4.4358 0.791746 4.68779 0.957009 4.90065 1.16625C5.1135 1.37549 5.28306 1.6246 5.39963 1.89937C5.51621 2.17414 5.57752 2.46918 5.58007 2.76765C5.57492 3.37068 5.33061 3.94701 4.90081 4.37003C4.47101 4.79305 3.89087 5.02816 3.28784 5.02372C2.6848 5.02816 2.10466 4.79305 1.67486 4.37003C1.24506 3.94701 1.00075 3.37068 0.995605 2.76765C0.998152 2.46918 1.05946 2.17414 1.17604 1.89937C1.29261 1.6246 1.46217 1.37549 1.67503 1.16625C1.88788 0.957009 2.13987 0.791746 2.41659 0.679895C2.69332 0.568045 2.98937 0.511798 3.28784 0.514366Z" fill="#3E484C"/> <path d="M6.24202 0.622751H9.61917C14.8657 0.750715 19.2972 4.96519 19.2972 10.1533C19.2972 15.4054 14.9547 19.6811 9.61917 19.6839L5.63837 19.6394C6.89854 18.624 6.98199 16.5571 6.98756 16.1871V16.1315V15.2357H9.62751C10.9837 15.2409 12.2869 14.7094 13.2527 13.7572C14.2184 12.805 14.7683 11.5095 14.7823 10.1533C14.7823 7.34922 12.2452 5.06812 9.39662 5.06812H6.15022C6.65975 4.44274 6.94555 3.66495 6.96218 2.85845C6.97882 2.05195 6.72533 1.26305 6.24202 0.617188V0.622751Z" fill="#3E484C"/> <path d="M5.31862 7.14062H5.55229V15.934C5.56354 16.4751 5.48649 17.0144 5.32418 17.5308C5.22842 17.8203 5.08862 18.0933 4.90969 18.3403C4.26152 19.2277 3.06255 19.7312 1.01512 19.6783V10.8905C0.980231 10.0981 1.17332 9.3122 1.57149 8.62612C2.19184 7.65248 3.41028 7.08499 5.55507 7.14619L5.31862 7.14062Z" fill="#3E484C"/> </svg> </div> <h4>Analysis</h4> </a> <a class="is-show nav-item genomic" href="#genomic-epidemiology"> <div class="icon"> <svg xmlns="http://www.w3.org/2000/svg" width="26" height="25" viewBox="0 0 26 25" fill="none"> <g clip-path="url(#clip0_187_2277)"> <path d="M23.5633 16.5457H19.3151V21.0372H23.2598" stroke="#969DA0" stroke-width="1.0479" stroke-linecap="round"/> <path d="M15.5599 6.41052H6.00145V15.9767H11.6721" stroke="#969DA0" stroke-width="1.0479" stroke-linecap="round"/> <path d="M5.76894 11.1937H1.25522" stroke="#969DA0" stroke-width="1.0479" stroke-linecap="round"/> <path d="M23.5632 4.52167H15.5599V8.56927H22.9916" stroke="#969DA0" stroke-width="1.0479" stroke-linecap="round"/> <path d="M23.4115 12.5344H11.7669L11.7669 18.7023H19.2392" stroke="#969DA0" stroke-width="1.0479" stroke-linecap="round"/> <circle cx="23.9948" cy="4.27377" r="1.1675" fill="#969DA0"/> <circle cx="23.9948" cy="8.3868" r="1.1675" fill="#969DA0"/> <circle cx="23.9948" cy="12.5001" r="1.1675" fill="#969DA0"/> <circle cx="23.9948" cy="16.6131" r="1.1675" fill="#969DA0"/> <circle cx="23.9948" cy="20.7264" r="1.1675" fill="#969DA0"/> </g> <defs> <clipPath id="clip0_187_2277"> <rect width="25" height="25" fill="white" transform="translate(0.708771)"/> </clipPath> </defs> </svg> </div> <h4>Genomic Epidemiology</h4> </a> <a class="is-show nav-item additional-materals" href="#additional-materials"> <div class="icon"> <svg width="25" height="23" viewBox="0 0 25 23" fill="none" xmlns="http://www.w3.org/2000/svg"> <path d="M9.03198 18.5991H1.65698C1.1047 18.5991 0.656982 18.1514 0.656982 17.5991V1.59912C0.656982 1.04684 1.1047 0.599121 1.65698 0.599121H16.657C17.2093 0.599121 17.657 1.04684 17.657 1.59912V6.85266" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.15698 4.59912H13.157" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M4.15698 7.59912H13.157" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M4.15698 10.5991H10.636" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M4.15698 13.5991H8.83626" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path fill-rule="evenodd" clip-rule="evenodd" d="M17.636 21.5991C20.9497 21.5991 23.636 18.9128 23.636 15.5991C23.636 12.2854 20.9497 9.59912 17.636 9.59912C14.3223 9.59912 11.636 12.2854 11.636 15.5991C11.636 18.9128 14.3223 21.5991 17.636 21.5991Z" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M17.636 12.5991V18.5991" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> <path d="M20.636 15.5991H14.636" stroke="#3E484C" stroke-linecap="round" stroke-linejoin="round"/> </svg> </div> <h4>Additional Materials</h4> </a> </div> <div class="filter--wrap"> <p class="filter-title">Filter by:</p> <ul class="filter-box"> <div class="dropdown-icon"> <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 18 11" 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stroke-linejoin="round"/> <path d="M6.79688 18.328V16.4045" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.68213 18.3282V13.5194" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.5674 18.3281V15.4429" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M21.2229 18.3281V11.5958" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.3376 18.3281V14.0002" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M15.4524 18.3281V9.67236" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Metagenomic sequencing (mNGS): introduction and lab setup</p> </a> </div> <div class="item is-link" data-cat="google-slides-presentation" data-recent=""> <a class="title" href="https://docs.google.com/presentation/d/1xyfMVyUs-l_0_2SlUU4VP0BmaTwgqZdjMDSvdZicRdQ/edit#slide=id.gaafdd68345_1_3" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M2.94971 6.8252C2.94971 6.27291 3.39742 5.8252 3.94971 5.8252H24.07C24.6223 5.8252 25.07 6.27291 25.07 6.8252V21.175C25.07 21.7273 24.6223 22.175 24.07 22.175H3.94971C3.39742 22.175 2.94971 21.7273 2.94971 21.175V6.8252Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.79688 18.328V16.4045" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.68213 18.3282V13.5194" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.5674 18.3281V15.4429" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M21.2229 18.3281V11.5958" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.3376 18.3281V14.0002" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M15.4524 18.3281V9.67236" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Introduction to Illumina sequencing and data analysis for mNGS using CZ ID</p> </a> </div> <div class="item is-link" data-cat="web-page" data-recent="recently-added"> <a class="title" href="https://chanzuckerberg.zendesk.com/hc/en-us/articles/360050963352-A-guide-to-BLAST" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M25.07 6.78685V21.2131C25.07 22.2755 24.2088 23.1366 23.1465 23.1366H4.87321C3.81089 23.1366 2.94971 22.2755 2.94971 21.2131V6.78685C2.94971 5.72452 3.81089 4.86334 4.87321 4.86334H23.1465C24.2088 4.86334 25.07 5.72452 25.07 6.78685Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M2.94971 9.67212H25.07" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.55587 6.78668C6.68866 6.78668 6.79631 6.89433 6.79631 7.02712C6.79631 7.15991 6.68866 7.26756 6.55587 7.26756C6.42308 7.26756 6.31543 7.15991 6.31543 7.02712C6.31543 6.89433 6.42308 6.78668 6.55587 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.4421 6.78668C9.57489 6.78668 9.68254 6.89433 9.68254 7.02712C9.68254 7.15991 9.57489 7.26756 9.4421 7.26756C9.30931 7.26756 9.20166 7.15991 9.20166 7.02712C9.20166 6.89433 9.30931 6.78668 9.4421 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.3271 6.78668C12.4599 6.78668 12.5675 6.89433 12.5675 7.02712C12.5675 7.15991 12.4599 7.26756 12.3271 7.26756C12.1943 7.26756 12.0867 7.15991 12.0867 7.02712C12.0867 6.89433 12.1943 6.78668 12.3271 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 13.5192H10.1628" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 16.4043H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 19.2895H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <rect x="15.9785" y="12.9792" width="6.125" height="6.79131" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>A guide to BLAST</p> </a> </div> </div> </div> <div class="is-show-sec content" id="study-design"> <h2>Study Design</h2> <div class="list-wrap"> <div class="item is-link" data-cat="google-slides-presentation" data-recent=""> <a class="title" href="https://docs.google.com/presentation/d/1Dd9_Zq-05aas55Ll0fFDuuzjGkoD3KaaLvqd1Qkek_I/edit#slide=id.p" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M2.94971 6.8252C2.94971 6.27291 3.39742 5.8252 3.94971 5.8252H24.07C24.6223 5.8252 25.07 6.27291 25.07 6.8252V21.175C25.07 21.7273 24.6223 22.175 24.07 22.175H3.94971C3.39742 22.175 2.94971 21.7273 2.94971 21.175V6.8252Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.79688 18.328V16.4045" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.68213 18.3282V13.5194" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.5674 18.3281V15.4429" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M21.2229 18.3281V11.5958" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.3376 18.3281V14.0002" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M15.4524 18.3281V9.67236" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>mNGS: study design and sample preparation</p> </a> </div> </div> </div> <div class="is-show-sec content" id="mngs-protocols"> <h2>Metagenomic next-generation sequencing (mNGS) protocols</h2> <div class="list-wrap"> <div class="item is-link" data-cat="google-doc" data-recent=""> <a class="title" href="https://docs.google.com/document/d/1RtNQc1D4or_ys7OxCCBjh4SDIdy7JaI4IE7if8EkHgE/edit#bookmark=id.ie7jj5g6q2f7" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M22.8641 6.78683C23.0444 6.96715 23.1458 7.21174 23.1459 7.46679V24.0984C23.1459 24.6295 22.7153 25.0601 22.1841 25.0601H5.83431C5.30315 25.0601 4.87256 24.6295 4.87256 24.0984V3.90157C4.87256 3.37041 5.30315 2.93982 5.83431 2.93982H18.6189C18.8739 2.93987 19.1185 3.04124 19.2988 3.22161L22.8641 6.78683Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 17.847H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 20.7322H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 14.9619H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 12.0764H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 9.19122H14.9715" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 9.19122H14.9715" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 12.0764H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 14.9619H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 17.847H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 20.7322H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Sample collection protocols</p> </a> </div> <div class="item is-link" data-cat="google-doc" data-recent=""> <a class="title" href="https://docs.google.com/document/d/1RtNQc1D4or_ys7OxCCBjh4SDIdy7JaI4IE7if8EkHgE/edit#bookmark=id.3qntryun7kes" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M22.8641 6.78683C23.0444 6.96715 23.1458 7.21174 23.1459 7.46679V24.0984C23.1459 24.6295 22.7153 25.0601 22.1841 25.0601H5.83431C5.30315 25.0601 4.87256 24.6295 4.87256 24.0984V3.90157C4.87256 3.37041 5.30315 2.93982 5.83431 2.93982H18.6189C18.8739 2.93987 19.1185 3.04124 19.2988 3.22161L22.8641 6.78683Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 17.847H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 20.7322H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 14.9619H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 12.0764H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 9.19122H14.9715" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 9.19122H14.9715" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 12.0764H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 14.9619H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 17.847H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 20.7322H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Illumina mNGS protocols</p> </a> </div> <div class="item is-link" data-cat="google-doc" data-recent=""> <a class="title" href="https://docs.google.com/document/d/1m1GAYVJLR2WueXbKJRGtXC2HRtq9rfFpHO802sllTvg/edit" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M22.8641 6.78683C23.0444 6.96715 23.1458 7.21174 23.1459 7.46679V24.0984C23.1459 24.6295 22.7153 25.0601 22.1841 25.0601H5.83431C5.30315 25.0601 4.87256 24.6295 4.87256 24.0984V3.90157C4.87256 3.37041 5.30315 2.93982 5.83431 2.93982H18.6189C18.8739 2.93987 19.1185 3.04124 19.2988 3.22161L22.8641 6.78683Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 17.847H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 20.7322H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 14.9619H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 12.0764H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 9.19122H14.9715" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 9.19122H14.9715" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 12.0764H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 14.9619H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 17.847H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M8.23926 20.7322H19.7803" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Oxford Nanopore mNGS protocols</p> </a> </div> <div class="item is-link" data-cat="google-slides-presentation" data-recent=""> <a class="title" href="https://docs.google.com/presentation/d/1OhjtYif9kstAai704MjhMeS8vNbawHh8h3FFBgpUT8k/edit#slide=id.p" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M2.94971 6.8252C2.94971 6.27291 3.39742 5.8252 3.94971 5.8252H24.07C24.6223 5.8252 25.07 6.27291 25.07 6.8252V21.175C25.07 21.7273 24.6223 22.175 24.07 22.175H3.94971C3.39742 22.175 2.94971 21.7273 2.94971 21.175V6.8252Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.79688 18.328V16.4045" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.68213 18.3282V13.5194" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.5674 18.3281V15.4429" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M21.2229 18.3281V11.5958" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.3376 18.3281V14.0002" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M15.4524 18.3281V9.67236" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Illumina library preparation for mNGS</p> </a> </div> <div class="item is-link" data-cat="google-slides-presentation" data-recent=""> <a class="title" href="https://docs.google.com/presentation/d/1KmtF_oCH7HzVVRdtB2ODl2Fnz9Wl-b8cP6A7w2vV7OQ/edit#slide=id.ge1f6c4c711_0_677" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M2.94971 6.8252C2.94971 6.27291 3.39742 5.8252 3.94971 5.8252H24.07C24.6223 5.8252 25.07 6.27291 25.07 6.8252V21.175C25.07 21.7273 24.6223 22.175 24.07 22.175H3.94971C3.39742 22.175 2.94971 21.7273 2.94971 21.175V6.8252Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.79688 18.328V16.4045" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.68213 18.3282V13.5194" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.5674 18.3281V15.4429" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M21.2229 18.3281V11.5958" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.3376 18.3281V14.0002" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M15.4524 18.3281V9.67236" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Illumina library quality control</p> </a> </div> </div> </div> <div class="is-show-sec content" id="enrichment-and-depletion"> <h2>Enrichment and depletion methods</h2> <div class="list-wrap"> <div class="item is-link" data-cat="google-slides-presentation" data-recent=""> <a class="title" href="https://docs.google.com/presentation/d/1SahiVZxVaCbn6Z62Va4193-dyZHvc3BG-htmnk6nYwo/edit#slide=id.p" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M2.94971 6.8252C2.94971 6.27291 3.39742 5.8252 3.94971 5.8252H24.07C24.6223 5.8252 25.07 6.27291 25.07 6.8252V21.175C25.07 21.7273 24.6223 22.175 24.07 22.175H3.94971C3.39742 22.175 2.94971 21.7273 2.94971 21.175V6.8252Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.79688 18.328V16.4045" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.68213 18.3282V13.5194" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.5674 18.3281V15.4429" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M21.2229 18.3281V11.5958" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.3376 18.3281V14.0002" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M15.4524 18.3281V9.67236" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Overview</p> </a> </div> <div class="item is-link" data-cat="google-slides-presentation" data-recent=""> <a class="title" href="https://docs.google.com/presentation/d/1ATnozUKGfEn_JbismR3OY-8A4bI1bxLEoOHFezYLF4Q/edit#slide=id.p" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M2.94971 6.8252C2.94971 6.27291 3.39742 5.8252 3.94971 5.8252H24.07C24.6223 5.8252 25.07 6.27291 25.07 6.8252V21.175C25.07 21.7273 24.6223 22.175 24.07 22.175H3.94971C3.39742 22.175 2.94971 21.7273 2.94971 21.175V6.8252Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.79688 18.328V16.4045" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.68213 18.3282V13.5194" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.5674 18.3281V15.4429" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M21.2229 18.3281V11.5958" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.3376 18.3281V14.0002" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M15.4524 18.3281V9.67236" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>FLASH protocol</p> </a> </div> <div class="item is-link" data-cat="web-page" data-recent=""> <a class="title" href="https://pubmed.ncbi.nlm.nih.gov/31114866/" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M25.07 6.78685V21.2131C25.07 22.2755 24.2088 23.1366 23.1465 23.1366H4.87321C3.81089 23.1366 2.94971 22.2755 2.94971 21.2131V6.78685C2.94971 5.72452 3.81089 4.86334 4.87321 4.86334H23.1465C24.2088 4.86334 25.07 5.72452 25.07 6.78685Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M2.94971 9.67212H25.07" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.55587 6.78668C6.68866 6.78668 6.79631 6.89433 6.79631 7.02712C6.79631 7.15991 6.68866 7.26756 6.55587 7.26756C6.42308 7.26756 6.31543 7.15991 6.31543 7.02712C6.31543 6.89433 6.42308 6.78668 6.55587 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.4421 6.78668C9.57489 6.78668 9.68254 6.89433 9.68254 7.02712C9.68254 7.15991 9.57489 7.26756 9.4421 7.26756C9.30931 7.26756 9.20166 7.15991 9.20166 7.02712C9.20166 6.89433 9.30931 6.78668 9.4421 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.3271 6.78668C12.4599 6.78668 12.5675 6.89433 12.5675 7.02712C12.5675 7.15991 12.4599 7.26756 12.3271 7.26756C12.1943 7.26756 12.0867 7.15991 12.0867 7.02712C12.0867 6.89433 12.1943 6.78668 12.3271 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 13.5192H10.1628" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 16.4043H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 19.2895H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <rect x="15.9785" y="12.9792" width="6.125" height="6.79131" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>FLASH</p> </a> </div> <div class="item is-link" data-cat="web-page" data-recent="recently-added"> <a class="title" href="https://www.protocols.io/view/dash-protocol-yxmvm7z99v3p/v4" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M25.07 6.78685V21.2131C25.07 22.2755 24.2088 23.1366 23.1465 23.1366H4.87321C3.81089 23.1366 2.94971 22.2755 2.94971 21.2131V6.78685C2.94971 5.72452 3.81089 4.86334 4.87321 4.86334H23.1465C24.2088 4.86334 25.07 5.72452 25.07 6.78685Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M2.94971 9.67212H25.07" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.55587 6.78668C6.68866 6.78668 6.79631 6.89433 6.79631 7.02712C6.79631 7.15991 6.68866 7.26756 6.55587 7.26756C6.42308 7.26756 6.31543 7.15991 6.31543 7.02712C6.31543 6.89433 6.42308 6.78668 6.55587 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.4421 6.78668C9.57489 6.78668 9.68254 6.89433 9.68254 7.02712C9.68254 7.15991 9.57489 7.26756 9.4421 7.26756C9.30931 7.26756 9.20166 7.15991 9.20166 7.02712C9.20166 6.89433 9.30931 6.78668 9.4421 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.3271 6.78668C12.4599 6.78668 12.5675 6.89433 12.5675 7.02712C12.5675 7.15991 12.4599 7.26756 12.3271 7.26756C12.1943 7.26756 12.0867 7.15991 12.0867 7.02712C12.0867 6.89433 12.1943 6.78668 12.3271 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 13.5192H10.1628" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 16.4043H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 19.2895H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <rect x="15.9785" y="12.9792" width="6.125" height="6.79131" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>DASH protocol</p> </a> </div> <div class="item is-link" data-cat="web-page" data-recent="recently-added"> <a class="title" href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0904-5" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M25.07 6.78685V21.2131C25.07 22.2755 24.2088 23.1366 23.1465 23.1366H4.87321C3.81089 23.1366 2.94971 22.2755 2.94971 21.2131V6.78685C2.94971 5.72452 3.81089 4.86334 4.87321 4.86334H23.1465C24.2088 4.86334 25.07 5.72452 25.07 6.78685Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M2.94971 9.67212H25.07" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.55587 6.78668C6.68866 6.78668 6.79631 6.89433 6.79631 7.02712C6.79631 7.15991 6.68866 7.26756 6.55587 7.26756C6.42308 7.26756 6.31543 7.15991 6.31543 7.02712C6.31543 6.89433 6.42308 6.78668 6.55587 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.4421 6.78668C9.57489 6.78668 9.68254 6.89433 9.68254 7.02712C9.68254 7.15991 9.57489 7.26756 9.4421 7.26756C9.30931 7.26756 9.20166 7.15991 9.20166 7.02712C9.20166 6.89433 9.30931 6.78668 9.4421 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.3271 6.78668C12.4599 6.78668 12.5675 6.89433 12.5675 7.02712C12.5675 7.15991 12.4599 7.26756 12.3271 7.26756C12.1943 7.26756 12.0867 7.15991 12.0867 7.02712C12.0867 6.89433 12.1943 6.78668 12.3271 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 13.5192H10.1628" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 16.4043H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 19.2895H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <rect x="15.9785" y="12.9792" width="6.125" height="6.79131" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>DASH publication</p> </a> </div> <div class="item is-link" data-cat="web-page" data-recent="recently-added"> <a class="title" href="https://www.protocols.io/view/in-vitro-transcription-for-dgrna-14egnxjepl5d/v2" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M25.07 6.78685V21.2131C25.07 22.2755 24.2088 23.1366 23.1465 23.1366H4.87321C3.81089 23.1366 2.94971 22.2755 2.94971 21.2131V6.78685C2.94971 5.72452 3.81089 4.86334 4.87321 4.86334H23.1465C24.2088 4.86334 25.07 5.72452 25.07 6.78685Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M2.94971 9.67212H25.07" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.55587 6.78668C6.68866 6.78668 6.79631 6.89433 6.79631 7.02712C6.79631 7.15991 6.68866 7.26756 6.55587 7.26756C6.42308 7.26756 6.31543 7.15991 6.31543 7.02712C6.31543 6.89433 6.42308 6.78668 6.55587 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.4421 6.78668C9.57489 6.78668 9.68254 6.89433 9.68254 7.02712C9.68254 7.15991 9.57489 7.26756 9.4421 7.26756C9.30931 7.26756 9.20166 7.15991 9.20166 7.02712C9.20166 6.89433 9.30931 6.78668 9.4421 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.3271 6.78668C12.4599 6.78668 12.5675 6.89433 12.5675 7.02712C12.5675 7.15991 12.4599 7.26756 12.3271 7.26756C12.1943 7.26756 12.0867 7.15991 12.0867 7.02712C12.0867 6.89433 12.1943 6.78668 12.3271 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 13.5192H10.1628" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 16.4043H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 19.2895H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <rect x="15.9785" y="12.9792" width="6.125" height="6.79131" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Guide RNA transcription (In Vitro Transcription for dgRNA V.2)</p> </a> </div> </div> </div> <div class="is-show-sec content" id="sequencing"> <h2>Sequencing</h2> <div class="list-wrap"> <div class="item is-link" data-cat="google-slides-presentation" data-recent="recently-added"> <a class="title" href="https://docs.google.com/presentation/d/163FHHlRWhQdcNP2wpe8WkrA0ay3vv3CKw0wYSsASOx0/edit#slide=id.p" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M2.94971 6.8252C2.94971 6.27291 3.39742 5.8252 3.94971 5.8252H24.07C24.6223 5.8252 25.07 6.27291 25.07 6.8252V21.175C25.07 21.7273 24.6223 22.175 24.07 22.175H3.94971C3.39742 22.175 2.94971 21.7273 2.94971 21.175V6.8252Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.79688 18.328V16.4045" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.68213 18.3282V13.5194" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.5674 18.3281V15.4429" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M21.2229 18.3281V11.5958" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.3376 18.3281V14.0002" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M15.4524 18.3281V9.67236" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>iSeq loading guide</p> </a> </div> <div class="item is-link" data-cat="google-slides-presentation" data-recent="recently-added"> <a class="title" href="https://docs.google.com/presentation/d/10fCGOuiPgwA0-R9BNDQaeJICOOywbVbv4-W109GMi7w/edit#slide=id.p" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M2.94971 6.8252C2.94971 6.27291 3.39742 5.8252 3.94971 5.8252H24.07C24.6223 5.8252 25.07 6.27291 25.07 6.8252V21.175C25.07 21.7273 24.6223 22.175 24.07 22.175H3.94971C3.39742 22.175 2.94971 21.7273 2.94971 21.175V6.8252Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.79688 18.328V16.4045" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.68213 18.3282V13.5194" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.5674 18.3281V15.4429" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M21.2229 18.3281V11.5958" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.3376 18.3281V14.0002" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M15.4524 18.3281V9.67236" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>MiSeq loading guide</p> </a> </div> </div> </div> <div class="is-show-sec content" id="quality-control"> <h2>Quality Control</h2> <div class="list-wrap"> <div class="item is-link" data-cat="web-page" data-recent="recently-added"> <a class="title" href="https://chanzuckerberg.zendesk.com/hc/en-us/articles/360053758913-Sample-QC" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M25.07 6.78685V21.2131C25.07 22.2755 24.2088 23.1366 23.1465 23.1366H4.87321C3.81089 23.1366 2.94971 22.2755 2.94971 21.2131V6.78685C2.94971 5.72452 3.81089 4.86334 4.87321 4.86334H23.1465C24.2088 4.86334 25.07 5.72452 25.07 6.78685Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M2.94971 9.67212H25.07" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.55587 6.78668C6.68866 6.78668 6.79631 6.89433 6.79631 7.02712C6.79631 7.15991 6.68866 7.26756 6.55587 7.26756C6.42308 7.26756 6.31543 7.15991 6.31543 7.02712C6.31543 6.89433 6.42308 6.78668 6.55587 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.4421 6.78668C9.57489 6.78668 9.68254 6.89433 9.68254 7.02712C9.68254 7.15991 9.57489 7.26756 9.4421 7.26756C9.30931 7.26756 9.20166 7.15991 9.20166 7.02712C9.20166 6.89433 9.30931 6.78668 9.4421 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.3271 6.78668C12.4599 6.78668 12.5675 6.89433 12.5675 7.02712C12.5675 7.15991 12.4599 7.26756 12.3271 7.26756C12.1943 7.26756 12.0867 7.15991 12.0867 7.02712C12.0867 6.89433 12.1943 6.78668 12.3271 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 13.5192H10.1628" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 16.4043H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 19.2895H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <rect x="15.9785" y="12.9792" width="6.125" height="6.79131" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Sample QC</p> </a> </div> <div class="item is-link" data-cat="google-slides-presentation" data-recent="recently-added"> <a class="title" href="https://docs.google.com/presentation/d/1FP0M5YdSeMmaKAD-ivwvcm2TJdcdz4rZOCfeoB8e2tA/edit#slide=id.gbe4c04d303_0_0" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M2.94971 6.8252C2.94971 6.27291 3.39742 5.8252 3.94971 5.8252H24.07C24.6223 5.8252 25.07 6.27291 25.07 6.8252V21.175C25.07 21.7273 24.6223 22.175 24.07 22.175H3.94971C3.39742 22.175 2.94971 21.7273 2.94971 21.175V6.8252Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.79688 18.328V16.4045" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.68213 18.3282V13.5194" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.5674 18.3281V15.4429" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M21.2229 18.3281V11.5958" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.3376 18.3281V14.0002" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M15.4524 18.3281V9.67236" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Sequencing Run QC</p> </a> </div> </div> </div> <div class="is-show-sec content" id="analysis"> <h2>Analysis</h2> <div class="list-wrap"> <div class="item is-link" data-cat="web-page" data-recent=""> <a class="title" href="https://czid.org/" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M25.07 6.78685V21.2131C25.07 22.2755 24.2088 23.1366 23.1465 23.1366H4.87321C3.81089 23.1366 2.94971 22.2755 2.94971 21.2131V6.78685C2.94971 5.72452 3.81089 4.86334 4.87321 4.86334H23.1465C24.2088 4.86334 25.07 5.72452 25.07 6.78685Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M2.94971 9.67212H25.07" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.55587 6.78668C6.68866 6.78668 6.79631 6.89433 6.79631 7.02712C6.79631 7.15991 6.68866 7.26756 6.55587 7.26756C6.42308 7.26756 6.31543 7.15991 6.31543 7.02712C6.31543 6.89433 6.42308 6.78668 6.55587 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.4421 6.78668C9.57489 6.78668 9.68254 6.89433 9.68254 7.02712C9.68254 7.15991 9.57489 7.26756 9.4421 7.26756C9.30931 7.26756 9.20166 7.15991 9.20166 7.02712C9.20166 6.89433 9.30931 6.78668 9.4421 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.3271 6.78668C12.4599 6.78668 12.5675 6.89433 12.5675 7.02712C12.5675 7.15991 12.4599 7.26756 12.3271 7.26756C12.1943 7.26756 12.0867 7.15991 12.0867 7.02712C12.0867 6.89433 12.1943 6.78668 12.3271 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 13.5192H10.1628" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 16.4043H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 19.2895H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <rect x="15.9785" y="12.9792" width="6.125" height="6.79131" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>CZ ID: The free, cloud-based metagenomics platform for researchers</p> </a> <ul> <li><a href="https://academic.oup.com/gigascience/article/9/10/giaa111/5918865" target="_blank" rel="noopener">Overview</a></li> <li><a href="https://chanzuckerberg.zendesk.com/hc/en-us/articles/13770737266196-Guide-to-mNGS-Data-Analysis" target="_blank" rel="noopener">Guide to data analysis on CZ ID</a></li> <li><a href="https://chanzuckerberg.zendesk.com/hc/en-us/articles/360035296573-Upload-mNGS-Illumina-Data-through-the-Web-App" target="_blank" rel="noopener">How to upload your data</a></li> <li><a href="https://chanzuckerberg.zendesk.com/hc/en-us/articles/14783973727636-Upload-Viral-Genome-Data-through-the-Web-App" target="_blank" rel="noopener">Guide to Viral Consensus Genome Generation from Amplicon Sequencing Data</a></li> <li><a href="https://chanzuckerberg.zendesk.com/hc/en-us/categories/12867564094612-FAQs" target="_blank" rel="noopener">FAQs</a></li> </ul> </div> <div class="item is-link" data-cat="web-page" data-recent="recently-added"> <a class="title" href="https://theiagenepi.org/" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M25.07 6.78685V21.2131C25.07 22.2755 24.2088 23.1366 23.1465 23.1366H4.87321C3.81089 23.1366 2.94971 22.2755 2.94971 21.2131V6.78685C2.94971 5.72452 3.81089 4.86334 4.87321 4.86334H23.1465C24.2088 4.86334 25.07 5.72452 25.07 6.78685Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M2.94971 9.67212H25.07" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.55587 6.78668C6.68866 6.78668 6.79631 6.89433 6.79631 7.02712C6.79631 7.15991 6.68866 7.26756 6.55587 7.26756C6.42308 7.26756 6.31543 7.15991 6.31543 7.02712C6.31543 6.89433 6.42308 6.78668 6.55587 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.4421 6.78668C9.57489 6.78668 9.68254 6.89433 9.68254 7.02712C9.68254 7.15991 9.57489 7.26756 9.4421 7.26756C9.30931 7.26756 9.20166 7.15991 9.20166 7.02712C9.20166 6.89433 9.30931 6.78668 9.4421 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.3271 6.78668C12.4599 6.78668 12.5675 6.89433 12.5675 7.02712C12.5675 7.15991 12.4599 7.26756 12.3271 7.26756C12.1943 7.26756 12.0867 7.15991 12.0867 7.02712C12.0867 6.89433 12.1943 6.78668 12.3271 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 13.5192H10.1628" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 16.4043H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 19.2895H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <rect x="15.9785" y="12.9792" width="6.125" height="6.79131" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>TheiaGenEpi: An open source, free, no-code genomic epidemiology analysis platform for public health</p> </a> <ul> <li><a href="https://theiagenepi.zendesk.com/hc/en-us/articles/29458732850971-TheiaGenEpi-overview" target="_blank" rel="noopener">Overview</a></li> <li><a href="https://theiagenepi.zendesk.com/hc/en-us/articles/29489952214299-Quick-guide-to-phylogenetic-tree-type" target="_blank" rel="noopener">Quick guide to phylogenetic tree types</a></li> <li><a href="https://theiagenepi.zendesk.com/hc/en-us" target="_blank" rel="noopener">TheiaGenEpi user guides</a></li> <li><a href="https://theiagenepi.zendesk.com/hc/en-us/sections/29433800234139-FAQ" target="_blank" rel="noopener">FAQs</a></li> </ul> </div> </div> </div> <div class="is-show-sec content" id="genomic-epidemiology"> <h2>Genomic Epidemiology Learning Center</h2> <div class="list-wrap"> <div class="item is-link" data-cat="web-page" data-recent=""> <a class="title" href="https://www.czbiohub.org/ebook/applied-genomic-epidemiology-handbook/" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M25.07 6.78685V21.2131C25.07 22.2755 24.2088 23.1366 23.1465 23.1366H4.87321C3.81089 23.1366 2.94971 22.2755 2.94971 21.2131V6.78685C2.94971 5.72452 3.81089 4.86334 4.87321 4.86334H23.1465C24.2088 4.86334 25.07 5.72452 25.07 6.78685Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M2.94971 9.67212H25.07" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.55587 6.78668C6.68866 6.78668 6.79631 6.89433 6.79631 7.02712C6.79631 7.15991 6.68866 7.26756 6.55587 7.26756C6.42308 7.26756 6.31543 7.15991 6.31543 7.02712C6.31543 6.89433 6.42308 6.78668 6.55587 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.4421 6.78668C9.57489 6.78668 9.68254 6.89433 9.68254 7.02712C9.68254 7.15991 9.57489 7.26756 9.4421 7.26756C9.30931 7.26756 9.20166 7.15991 9.20166 7.02712C9.20166 6.89433 9.30931 6.78668 9.4421 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.3271 6.78668C12.4599 6.78668 12.5675 6.89433 12.5675 7.02712C12.5675 7.15991 12.4599 7.26756 12.3271 7.26756C12.1943 7.26756 12.0867 7.15991 12.0867 7.02712C12.0867 6.89433 12.1943 6.78668 12.3271 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 13.5192H10.1628" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 16.4043H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 19.2895H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <rect x="15.9785" y="12.9792" width="6.125" height="6.79131" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p><em>The Applied Genomic Epidemiology Handbook</em></p> </a> </div> <div class="item " data-cat="web-page" data-recent=""> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M25.07 6.78685V21.2131C25.07 22.2755 24.2088 23.1366 23.1465 23.1366H4.87321C3.81089 23.1366 2.94971 22.2755 2.94971 21.2131V6.78685C2.94971 5.72452 3.81089 4.86334 4.87321 4.86334H23.1465C24.2088 4.86334 25.07 5.72452 25.07 6.78685Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M2.94971 9.67212H25.07" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.55587 6.78668C6.68866 6.78668 6.79631 6.89433 6.79631 7.02712C6.79631 7.15991 6.68866 7.26756 6.55587 7.26756C6.42308 7.26756 6.31543 7.15991 6.31543 7.02712C6.31543 6.89433 6.42308 6.78668 6.55587 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.4421 6.78668C9.57489 6.78668 9.68254 6.89433 9.68254 7.02712C9.68254 7.15991 9.57489 7.26756 9.4421 7.26756C9.30931 7.26756 9.20166 7.15991 9.20166 7.02712C9.20166 6.89433 9.30931 6.78668 9.4421 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.3271 6.78668C12.4599 6.78668 12.5675 6.89433 12.5675 7.02712C12.5675 7.15991 12.4599 7.26756 12.3271 7.26756C12.1943 7.26756 12.0867 7.15991 12.0867 7.02712C12.0867 6.89433 12.1943 6.78668 12.3271 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 13.5192H10.1628" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 16.4043H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 19.2895H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <rect x="15.9785" y="12.9792" width="6.125" height="6.79131" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Essential Background Theory for Genomic Epidemiology</p> <ul> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/mod1-timescales-pathogen-evolution-transmission/">Module 1: The overlapping timescales of pathogen evolution and transmission</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/mod2-sequences-trees/">Module 2: From sequences to trees</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/mod3-terminology-phylogenetic-trees/">Module 3: Shared terminology for describing phylogenetic trees.</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/mod4-evolutionary-rates-molecular-clocks-sequence-data/">Module 4: Estimating evolutionary rates (molecular clocks) from sequence data</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/mod5-interpreting-evolutionary-rates/">Module 5: Interpreting and working with evolutionary rates</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/mod6-evolutionary-rates-infer-time-trees/">Module 6: Using evolutionary rates to infer time trees</a></li> </ul> </div> <div class="item " data-cat="web-page" data-recent=""> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M25.07 6.78685V21.2131C25.07 22.2755 24.2088 23.1366 23.1465 23.1366H4.87321C3.81089 23.1366 2.94971 22.2755 2.94971 21.2131V6.78685C2.94971 5.72452 3.81089 4.86334 4.87321 4.86334H23.1465C24.2088 4.86334 25.07 5.72452 25.07 6.78685Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M2.94971 9.67212H25.07" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.55587 6.78668C6.68866 6.78668 6.79631 6.89433 6.79631 7.02712C6.79631 7.15991 6.68866 7.26756 6.55587 7.26756C6.42308 7.26756 6.31543 7.15991 6.31543 7.02712C6.31543 6.89433 6.42308 6.78668 6.55587 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.4421 6.78668C9.57489 6.78668 9.68254 6.89433 9.68254 7.02712C9.68254 7.15991 9.57489 7.26756 9.4421 7.26756C9.30931 7.26756 9.20166 7.15991 9.20166 7.02712C9.20166 6.89433 9.30931 6.78668 9.4421 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.3271 6.78668C12.4599 6.78668 12.5675 6.89433 12.5675 7.02712C12.5675 7.15991 12.4599 7.26756 12.3271 7.26756C12.1943 7.26756 12.0867 7.15991 12.0867 7.02712C12.0867 6.89433 12.1943 6.78668 12.3271 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 13.5192H10.1628" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 16.4043H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 19.2895H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <rect x="15.9785" y="12.9792" width="6.125" height="6.79131" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Practicing Gaining Epidemiological Insights from Genomic Data</p> <ul> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/sequence-alignments-molecular-clocks/">Genomic Epi Basics: Sequence alignments and molecular clocks</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/practice-reading-phylogenetic-trees/">Genomic Epi Basics: Practice reading phylogenetic trees</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/applying-mutation-report-disease-surveillance-work/">Applying the mutation report to disease surveillance work</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/assessing-linkages-between-covid-19-cases/">Epi Insights Part I: Assessing linkages between COVID-19 cases</a></li> </ul> </div> <div class="item " data-cat="web-page" data-recent=""> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M25.07 6.78685V21.2131C25.07 22.2755 24.2088 23.1366 23.1465 23.1366H4.87321C3.81089 23.1366 2.94971 22.2755 2.94971 21.2131V6.78685C2.94971 5.72452 3.81089 4.86334 4.87321 4.86334H23.1465C24.2088 4.86334 25.07 5.72452 25.07 6.78685Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M2.94971 9.67212H25.07" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.55587 6.78668C6.68866 6.78668 6.79631 6.89433 6.79631 7.02712C6.79631 7.15991 6.68866 7.26756 6.55587 7.26756C6.42308 7.26756 6.31543 7.15991 6.31543 7.02712C6.31543 6.89433 6.42308 6.78668 6.55587 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.4421 6.78668C9.57489 6.78668 9.68254 6.89433 9.68254 7.02712C9.68254 7.15991 9.57489 7.26756 9.4421 7.26756C9.30931 7.26756 9.20166 7.15991 9.20166 7.02712C9.20166 6.89433 9.30931 6.78668 9.4421 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.3271 6.78668C12.4599 6.78668 12.5675 6.89433 12.5675 7.02712C12.5675 7.15991 12.4599 7.26756 12.3271 7.26756C12.1943 7.26756 12.0867 7.15991 12.0867 7.02712C12.0867 6.89433 12.1943 6.78668 12.3271 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 13.5192H10.1628" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 16.4043H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 19.2895H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <rect x="15.9785" y="12.9792" width="6.125" height="6.79131" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Genomic Epidemiology Seminar Series Recordings</p> <ul> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season1-episode1/">Season 1, Episode 1</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season1-episode2">Season 1, Episode 2</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season1-episode3">Season 1, Episode 3</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season1-episode4">Season 1, Episode 4</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season1-episode5">Season 1, Episode 5</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season1-episode6">Season 1, Episode 6</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season1-episode7">Season 1, Episode 7</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season1-episode8">Season 1, Episode 8</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season1-episode9">Season 1, Episode 9</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season1-episode10">Season 1, Episode 10</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season1-episode11/">Season 1, Episode 11</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season1-episode12/">Season 1, Episode 12</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season1-episode13/">Season 1, Episode 13</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season1-episode14/">Season 1, Episode 14</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season1-episode15/">Season 1, Episode 15</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season2-episode1/">Season 2, Episode 1</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season2-episode2/">Season 2, Episode 2</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season2-episode3/">Season 2, Episode 3</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season2-episode4">Season 2, Episode 4</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season2-episode5">Season 2, Episode 5</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season2-episode6">Season 2, Episode 6</a></li> <li><a href="https://czbiohub.org/rapid-response/genomic-epidemiology/seminars-season2-episode7">Season 2, Episode 7</a></li> </ul> </div> </div> </div> <div class="is-show-sec content" id="additional-materials"> <h2>Additional Materials</h2> <div class="list-wrap"> <div class="item is-link" data-cat="google-slides-presentation" data-recent="recently-added"> <a class="title" href="https://docs.google.com/presentation/d/1O_kWfL-MQBRO0w84lxQxdBf-ooSpEUmUOyN-OqCecWk/edit#slide=id.g9ee72de1f0_0_0" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M2.94971 6.8252C2.94971 6.27291 3.39742 5.8252 3.94971 5.8252H24.07C24.6223 5.8252 25.07 6.27291 25.07 6.8252V21.175C25.07 21.7273 24.6223 22.175 24.07 22.175H3.94971C3.39742 22.175 2.94971 21.7273 2.94971 21.175V6.8252Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.79688 18.328V16.4045" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.68213 18.3282V13.5194" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.5674 18.3281V15.4429" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M21.2229 18.3281V11.5958" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.3376 18.3281V14.0002" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M15.4524 18.3281V9.67236" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>How to make your own SPRI beads</p> </a> </div> <div class="item is-link" data-cat="google-slides-presentation" data-recent="recently-added"> <a class="title" href="https://docs.google.com/presentation/d/1XKQgup3Jbi9PRtBlVBRZDjdypbd_KrYhqt-5ogGfVww/edit#slide=id.p" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M2.94971 6.8252C2.94971 6.27291 3.39742 5.8252 3.94971 5.8252H24.07C24.6223 5.8252 25.07 6.27291 25.07 6.8252V21.175C25.07 21.7273 24.6223 22.175 24.07 22.175H3.94971C3.39742 22.175 2.94971 21.7273 2.94971 21.175V6.8252Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.79688 18.328V16.4045" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.68213 18.3282V13.5194" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.5674 18.3281V15.4429" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M21.2229 18.3281V11.5958" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.3376 18.3281V14.0002" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M15.4524 18.3281V9.67236" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Sequencing SARS-CoV-2 for public health laboratories</p> </a> <ul> <li><a href="https://docs.google.com/presentation/d/1yQI8ZogC1dFjVq5nU5R7SgumOa1Wqg6K5Wqb2ofwF54/edit#slide=id.p1" target="_blank" rel="noopener">SARS-CoV2 Sequencing Strategies</a></li> <li><a href="https://www.protocols.io/view/sars-cov-2-enrichment-sequencing-by-spiked-primer-261geowedl47/v4" target="_blank" rel="noopener">SARS-CoV-2 metagenomic sequencing by spiked primer enrichment (MSSPE), library prep protocol</a></li> <li><a href="https://www.protocols.io/view/artic-neb-sars-cov-2-library-prep-bp2l6n69rgqe/v2" target="_blank" rel="noopener">SARS-CoV-2 ARTIC sequencing using Illumina, library prep protocol</a></li> <li><a href="https://docs.google.com/presentation/d/13jBHJxRcNedqsl_IGXAEjYfxk4FalPnnCajc4_AHpnc/edit#slide=id.p" target="_blank" rel="noopener">Host transcriptome analyses for SARS-CoV2</a></li> <li><a href="https://docs.google.com/presentation/d/10y2XhrRpHw5zHyytGethagPvPar700ZNyNzX6mIbzh4/edit#slide=id.p" target="_blank" rel="noopener">SARS-CoV2 Genome QC & Phylogenetics</a></li> </ul> </div> <div class="item is-link" data-cat="google-slides-presentation" data-recent=""> <a class="title" href="https://docs.google.com/presentation/d/1JW5kY8RzhhS1cJtJIZjdGHSoQf3Yk6vVycK52352x38/edit#slide=id.p" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M2.94971 6.8252C2.94971 6.27291 3.39742 5.8252 3.94971 5.8252H24.07C24.6223 5.8252 25.07 6.27291 25.07 6.8252V21.175C25.07 21.7273 24.6223 22.175 24.07 22.175H3.94971C3.39742 22.175 2.94971 21.7273 2.94971 21.175V6.8252Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.79688 18.328V16.4045" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.68213 18.3282V13.5194" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.5674 18.3281V15.4429" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M21.2229 18.3281V11.5958" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M18.3376 18.3281V14.0002" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M15.4524 18.3281V9.67236" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>Scaling sequencing</p> </a> </div> <div class="item is-link" data-cat="web-page" data-recent="recently-added"> <a class="title" href="https://chanzuckerberg.zendesk.com/hc/en-us/articles/360050963352-A-guide-to-BLAST" target="_blank"> <svg width="2.9rem" height="2.8rem" viewBox="0 0 29 28" fill="none" xmlns="http://www.w3.org/2000/svg"> <path fill-rule="evenodd" clip-rule="evenodd" d="M25.07 6.78685V21.2131C25.07 22.2755 24.2088 23.1366 23.1465 23.1366H4.87321C3.81089 23.1366 2.94971 22.2755 2.94971 21.2131V6.78685C2.94971 5.72452 3.81089 4.86334 4.87321 4.86334H23.1465C24.2088 4.86334 25.07 5.72452 25.07 6.78685Z" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M2.94971 9.67212H25.07" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M6.55587 6.78668C6.68866 6.78668 6.79631 6.89433 6.79631 7.02712C6.79631 7.15991 6.68866 7.26756 6.55587 7.26756C6.42308 7.26756 6.31543 7.15991 6.31543 7.02712C6.31543 6.89433 6.42308 6.78668 6.55587 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M9.4421 6.78668C9.57489 6.78668 9.68254 6.89433 9.68254 7.02712C9.68254 7.15991 9.57489 7.26756 9.4421 7.26756C9.30931 7.26756 9.20166 7.15991 9.20166 7.02712C9.20166 6.89433 9.30931 6.78668 9.4421 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M12.3271 6.78668C12.4599 6.78668 12.5675 6.89433 12.5675 7.02712C12.5675 7.15991 12.4599 7.26756 12.3271 7.26756C12.1943 7.26756 12.0867 7.15991 12.0867 7.02712C12.0867 6.89433 12.1943 6.78668 12.3271 6.78668" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 13.5192H10.1628" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 16.4043H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <path d="M5.83496 19.2895H13.0481" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> <rect x="15.9785" y="12.9792" width="6.125" height="6.79131" stroke="#00A3E0" stroke-linecap="round" stroke-linejoin="round"/> </svg> <p>A guide to BLAST</p> </a> </div> </div> </div> </div> </div> </div> </section> </div>  <footer class="footer" role="contentinfo" id="footer"> <div class="footer__top"> <div class="footer__about"> <span class="footer__brand"> <a href="/sf/"> <img src="https://www.czbiohub.org/rapid-response/wp-content/themes/czbiohub/img/sf-footer-logo.png" alt="Footer Logo" style="max-width: 24.1rem" /> </a> </span> <div 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