CINXE.COM

<!DOCTYPE html> <html class="writer-html5" lang="en"> <head> <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" /> <meta name="viewport" content="width=device-width, initial-scale=1.0" /> <title>Tutorials | BV-BRC</title> <link rel="stylesheet" type="text/css" href="../_static/pygments.css" /> <link rel="stylesheet" type="text/css" href="../_static/css/theme.css" /> <link rel="stylesheet" type="text/css" href="../_static/css/custom.css" /> <link rel="shortcut icon" href="../_static/favicon.ico"/>  <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script> <script src="../_static/jquery.js"></script> <script src="../_static/underscore.js"></script> <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script> <script src="../_static/doctools.js"></script> <script src="../_static/sphinx_highlight.js"></script> <script src="../_static/js/theme.js"></script> <link rel="author" title="About these documents" href="../about.html" /> <link rel="index" title="Index" href="../genindex.html" /> <link rel="search" title="Search" href="../search.html" /> <link rel="next" title="Genome Assembly Service" href="genome_assembly/assembly.html" /> <link rel="prev" title="FTP Site" href="../quick_references/ftp.html" /> <meta name="google-site-verification" content="TkjceNtwo7upCQl_gx8Zmhhp9tCmc08LitZGuvQ1Eb8" /> <link rel="icon" sizes="16x16 32x32" href="/_static/favicon.ico" /> <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Lato:400,400i,700|Roboto:400,700&display=swap"> <title>Tutorials | BV-BRC</title> </head> <body class="wy-body-for-nav"> <div class="wy-grid-for-nav"> <nav data-toggle="wy-nav-shift" class="wy-nav-side"> <div class="wy-side-scroll"> <div class="wy-side-nav-search" style="background: #e3e3e3" > <a href="../index.html"> </a> <div role="search"> <form id="rtd-search-form" class="wy-form" action="https://www.google.com/search" method="get" target="bvbrc_docs_search"> <input type="text" name="q" placeholder="Search docs" /> <input type="hidden" name="sitesearch" value="bv-brc.org" /> </form> </div> </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu"> <p class="caption" role="heading"><span class="caption-text">Updates and Reports</span></p> <ul> <li class="toctree-l1"><a class="reference internal" href="../news/index.html">News and Announcements</a></li> <li class="toctree-l1"><a class="reference internal" href="../reports_and_analysis/index.html">Reports and Analysis</a></li> </ul> <p class="caption" role="heading"><span class="caption-text">Help Resources:</span></p> <ul class="current"> <li class="toctree-l1"><a class="reference internal" href="../overview.html">Overview</a></li> <li class="toctree-l1"><a class="reference internal" href="../quick_start/index.html">Quick Start</a></li> <li class="toctree-l1"><a class="reference internal" href="../data_protocols/index.html">Data Sources and Protocols</a></li> <li class="toctree-l1"><a class="reference internal" href="../quick_references/index.html">Quick Reference Guides</a></li> <li class="toctree-l1 current"><a class="current reference internal" href="#">Tutorials</a><ul> <li class="toctree-l2"><a class="reference internal" href="#genomics">Genomics</a><ul> <li class="toctree-l3"><a class="reference internal" href="genome_assembly/assembly.html">Genome Assembly Service</a></li> <li class="toctree-l3"><a class="reference internal" href="genome_annotation/genome_annotation.html">Genome Annotation Service</a></li> <li class="toctree-l3"><a class="reference internal" href="comprehensive_genome_analysis/comprehensive_genome_analysis.html">Comprehensive Genome Analysis (CGA) Service</a></li> <li class="toctree-l3"><a class="reference internal" href="blast/blast.html">BLAST Service</a></li> <li class="toctree-l3"><a class="reference internal" href="primer_design/primer_design.html">Primer Design Service</a></li> <li class="toctree-l3"><a class="reference internal" href="similar_genome_finder/similar_genome_finder.html">Similar Genome Finder Service</a></li> <li class="toctree-l3"><a class="reference internal" href="genome_alignment/genome_alignment.html">Genome Alignment Service</a></li> <li class="toctree-l3"><a class="reference internal" href="variation_analysis/variation_analysis.html">Variation - SNP Analysis Service</a></li> <li class="toctree-l3"><a class="reference internal" href="tn-seq/tn-seq.html">Tn-Seq Analysis Service</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="#phylogenomics-services">Phylogenomics Services</a><ul> <li class="toctree-l3"><a class="reference internal" href="phylogenetic_tree/phylogenetic_tree.html">Bacterial Phylogenetic Tree Service</a></li> <li class="toctree-l3"><a class="reference internal" href="genetree/genetree.html">Gene Tree Service</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="#protein-tools">Protein Tools</a><ul> <li class="toctree-l3"><a class="reference internal" href="msa_snp_variation/msa_snp_variation.html">MSA and SNP/Variation Analysis Service</a></li> <li class="toctree-l3"><a class="reference internal" href="metacats/metacats.html">Metadata-driven Comparative Analysis Tool (Meta-CATS)</a></li> <li class="toctree-l3"><a class="reference internal" href="proteome_comparison/proteome_comparison.html">Proteome Comparison Service</a></li> <li class="toctree-l3"><a class="reference internal" href="comparative_systems/comparative_systems.html">Comparative Systems Service</a></li> <li class="toctree-l3"><a class="reference internal" href="docking/docking.html">Small Molecule Ligand Docking Service</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="#metagenomics">Metagenomics</a><ul> <li class="toctree-l3"><a class="reference internal" href="taxonomic_classification/taxonomic_classification.html">Taxonomic Classification Service</a></li> <li class="toctree-l3"><a class="reference internal" href="metagenomic_binning/metagenomic_binning.html">Metagenomic Binning Service</a></li> <li class="toctree-l3"><a class="reference internal" href="metagenomic_read_mapping/metagenomic_read_mapping.html">Metagenomic Read Mapping</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="#transcriptomics">Transcriptomics</a><ul> <li class="toctree-l3"><a class="reference internal" href="rna_seq/rna_seq.html">RNA-Seq Analysis Service</a></li> <li class="toctree-l3"><a class="reference internal" href="expression_import/expression_import.html">Expression Import Service</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="#utilities">Utilities</a><ul> <li class="toctree-l3"><a class="reference internal" href="fastq_utilities/fastq_utilities.html">Fastq Utilities Service</a></li> <li class="toctree-l3"><a class="reference internal" href="id_mapper/id_mapper.html">ID Mapper Tool</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="#viral-services">Viral Services</a><ul> <li class="toctree-l3"><a class="reference internal" href="sars_cov_2_assembly_annotation/sars_cov_2_assembly_annotation.html">SARS-CoV-2 Genome Assembly and Annotation Service</a></li> <li class="toctree-l3"><a class="reference internal" href="sars_cov_2_wastewater/sars_cov_2_wastewater.html">SARS-Cov-2 Wastewater Analysis Service</a></li> <li class="toctree-l3"><a class="reference internal" href="sequence_submission/sequence_submission.html">Sequence Submission Service</a></li> <li class="toctree-l3"><a class="reference internal" href="ha_numbering/ha_numbering.html">HA Subtype Numbering Conversion Service</a></li> <li class="toctree-l3"><a class="reference internal" href="subspecies_classification/subspecies_classification.html">Subspecies Classification Service</a></li> <li class="toctree-l3"><a class="reference internal" href="viral_assembly/assembly.html">Analyzing Viral Genome Assembly Using BV-BRC Tools Tutorial</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="#data-visualizations">Data Visualizations</a><ul> <li class="toctree-l3"><a class="reference internal" href="compare_region_viewer/compare_region_viewer.html">Compare Region Viewer</a></li> </ul> </li> </ul> </li> <li class="toctree-l1"><a class="reference internal" href="../cli_tutorial/index.html">Command Line Interface</a></li> <li class="toctree-l1"><a class="reference internal" href="../videos/index.html">Instructional Videos</a></li> <li class="toctree-l1"><a class="reference internal" href="../webinar/index.html">Webinars</a></li> <li class="toctree-l1"><a class="reference internal" href="../workshops/index.html">Workshops</a></li> </ul> <p class="caption" role="heading"><span class="caption-text">System Documentation:</span></p> <ul> <li class="toctree-l1"><a class="reference internal" href="../system_documentation/data_management_sharing.html">Data Management and Sharing</a></li> <li class="toctree-l1"><a class="reference internal" href="../system_documentation/data.html">Data</a></li> <li class="toctree-l1"><a class="reference internal" href="../system_documentation/database.html">Database</a></li> <li class="toctree-l1"><a class="reference internal" href="../system_documentation/capabilities_and_functionality.html">Capabilities And Functionality</a></li> <li class="toctree-l1"><a class="reference internal" href="../system_documentation/software_tools_and_code.html">Software Tools And Code</a></li> <li class="toctree-l1"><a class="reference internal" href="../system_documentation/system_architecture.html">System Architecture</a></li> <li class="toctree-l1"><a class="reference internal" href="../system_documentation/documentation.html">Documentation</a></li> <li class="toctree-l1"><a class="reference internal" href="../system_documentation/accounts.html">Accounts</a></li> <li class="toctree-l1"><a class="reference internal" href="../test_procedures/index.html">Test Procedures</a></li> <li class="toctree-l1"><a class="reference internal" href="../usage_metrics.html">Usage Metrics</a></li> </ul> </div> </div> </nav> <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" style="background: #e3e3e3" > <i data-toggle="wy-nav-top" class="fa fa-bars"></i> <a href="../index.html">BV-BRC</a> </nav> <div class="wy-nav-content"> <div class="rst-content"> <div role="navigation" aria-label="Page navigation"> <ul class="wy-breadcrumbs"> <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li> <li class="breadcrumb-item active">Tutorials</li> <li class="wy-breadcrumbs-aside">  <a href="https://github.com/BV-BRC/bvbrc_docs/blob/master/docroot/tutorial/index.rst" class="fa fa-github"> Edit on GitHub</a> </li> </ul> <hr/> </div> <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> <div itemprop="articleBody"> <section id="tutorials"> <h1>Tutorials<a class="headerlink" href="#tutorials" title="Permalink to this heading">露</a></h1> <p>The BV-BRC website provides the capability to perform a broad array of analyses. These <strong>Tutorials</strong> provide step-by-step instructions for performing common tasks and analyses using the website. The examples are chosen to also provide a relevant biological context to help deomonstrate utility and interpretation of the data and results.</p> <section id="genomics"> <h2>Genomics<a class="headerlink" href="#genomics" title="Permalink to this heading">露</a></h2> <div class="toctree-wrapper compound"> <ul> <li class="toctree-l1"><a class="reference internal" href="genome_assembly/assembly.html">Genome Assembly Service</a></li> <li class="toctree-l1"><a class="reference internal" href="genome_annotation/genome_annotation.html">Genome Annotation Service</a></li> <li class="toctree-l1"><a class="reference internal" href="comprehensive_genome_analysis/comprehensive_genome_analysis.html">Comprehensive Genome Analysis (CGA) Service</a></li> <li class="toctree-l1"><a class="reference internal" href="blast/blast.html">BLAST Service</a></li> <li class="toctree-l1"><a class="reference internal" href="primer_design/primer_design.html">Primer Design Service</a></li> <li class="toctree-l1"><a class="reference internal" href="similar_genome_finder/similar_genome_finder.html">Similar Genome Finder Service</a></li> <li class="toctree-l1"><a class="reference internal" href="genome_alignment/genome_alignment.html">Genome Alignment Service</a></li> <li class="toctree-l1"><a class="reference internal" href="variation_analysis/variation_analysis.html">Variation - SNP Analysis Service</a></li> <li class="toctree-l1"><a class="reference internal" href="tn-seq/tn-seq.html">Tn-Seq Analysis Service</a></li> </ul> </div> </section> <section id="phylogenomics-services"> <h2>Phylogenomics Services<a class="headerlink" href="#phylogenomics-services" title="Permalink to this heading">露</a></h2> <div class="toctree-wrapper compound"> <ul> <li class="toctree-l1"><a class="reference internal" href="phylogenetic_tree/phylogenetic_tree.html">Bacterial Phylogenetic Tree Service</a></li> <li class="toctree-l1"><a class="reference internal" href="genetree/genetree.html">Gene Tree Service</a></li> </ul> </div> </section> <section id="protein-tools"> <h2>Protein Tools<a class="headerlink" href="#protein-tools" title="Permalink to this heading">露</a></h2> <div class="toctree-wrapper compound"> <ul> <li class="toctree-l1"><a class="reference internal" href="msa_snp_variation/msa_snp_variation.html">MSA and SNP/Variation Analysis Service</a></li> <li class="toctree-l1"><a class="reference internal" href="metacats/metacats.html">Metadata-driven Comparative Analysis Tool (Meta-CATS)</a></li> <li class="toctree-l1"><a class="reference internal" href="proteome_comparison/proteome_comparison.html">Proteome Comparison Service</a></li> <li class="toctree-l1"><a class="reference internal" href="comparative_systems/comparative_systems.html">Comparative Systems Service</a></li> <li class="toctree-l1"><a class="reference internal" href="docking/docking.html">Small Molecule Ligand Docking Service</a></li> </ul> </div> </section> <section id="metagenomics"> <h2>Metagenomics<a class="headerlink" href="#metagenomics" title="Permalink to this heading">露</a></h2> <div class="toctree-wrapper compound"> <ul> <li class="toctree-l1"><a class="reference internal" href="taxonomic_classification/taxonomic_classification.html">Taxonomic Classification Service</a></li> <li class="toctree-l1"><a class="reference internal" href="metagenomic_binning/metagenomic_binning.html">Metagenomic Binning Service</a></li> <li class="toctree-l1"><a class="reference internal" href="metagenomic_read_mapping/metagenomic_read_mapping.html">Metagenomic Read Mapping</a></li> </ul> </div> </section> <section id="transcriptomics"> <h2>Transcriptomics<a class="headerlink" href="#transcriptomics" title="Permalink to this heading">露</a></h2> <div class="toctree-wrapper compound"> <ul> <li class="toctree-l1"><a class="reference internal" href="rna_seq/rna_seq.html">RNA-Seq Analysis Service</a></li> <li class="toctree-l1"><a class="reference internal" href="expression_import/expression_import.html">Expression Import Service</a></li> </ul> </div> </section> <section id="utilities"> <h2>Utilities<a class="headerlink" href="#utilities" title="Permalink to this heading">露</a></h2> <div class="toctree-wrapper compound"> <ul> <li class="toctree-l1"><a class="reference internal" href="fastq_utilities/fastq_utilities.html">Fastq Utilities Service</a></li> <li class="toctree-l1"><a class="reference internal" href="id_mapper/id_mapper.html">ID Mapper Tool</a></li> </ul> </div> </section> <section id="viral-services"> <h2>Viral Services<a class="headerlink" href="#viral-services" title="Permalink to this heading">露</a></h2> <div class="toctree-wrapper compound"> <ul> <li class="toctree-l1"><a class="reference internal" href="sars_cov_2_assembly_annotation/sars_cov_2_assembly_annotation.html">SARS-CoV-2 Genome Assembly and Annotation Service</a></li> <li class="toctree-l1"><a class="reference internal" href="sars_cov_2_wastewater/sars_cov_2_wastewater.html">SARS-Cov-2 Wastewater Analysis Service</a></li> <li class="toctree-l1"><a class="reference internal" href="sequence_submission/sequence_submission.html">Sequence Submission Service</a></li> <li class="toctree-l1"><a class="reference internal" href="ha_numbering/ha_numbering.html">HA Subtype Numbering Conversion Service</a></li> <li class="toctree-l1"><a class="reference internal" href="subspecies_classification/subspecies_classification.html">Subspecies Classification Service</a></li> <li class="toctree-l1"><a class="reference internal" href="viral_assembly/assembly.html">Analyzing Viral Genome Assembly Using BV-BRC Tools Tutorial</a></li> </ul> </div> </section> <section id="data-visualizations"> <h2>Data Visualizations<a class="headerlink" href="#data-visualizations" title="Permalink to this heading">露</a></h2> <div class="toctree-wrapper compound"> <ul> <li class="toctree-l1"><a class="reference internal" href="compare_region_viewer/compare_region_viewer.html">Compare Region Viewer</a></li> </ul> </div> </section> </section> </div> </div> <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer"> <a href="../quick_references/ftp.html" class="btn btn-neutral float-left" title="FTP Site" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a> <a href="genome_assembly/assembly.html" class="btn btn-neutral float-right" title="Genome Assembly Service" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a> </div> <hr/> <div role="contentinfo"> <p>© Copyright 2023 | The BV-BRC Team.</p> </div> Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. </footer> </div> </div> </section> </div> <script> jQuery(function () { SphinxRtdTheme.Navigation.enable(true); }); </script> <script> var logo = '<img src="https://www.bv-brc.org/docs/_static/bvbrc-logo-blue.png" class="logo" alt="BV-BRC Logo">'; var home = '<div class="branding"><a href="https://bv-brc.org" title="BV-BRC Homepage">BV-BRC Home</a> &rsaquo; <a href="/docs/" title="BV-BRC Documentation">Docs</a></div>'; $(".wy-side-nav-search").prepend(home).prepend(logo); </script>  <script async src="https://www.googletagmanager.com/gtag/js?id=G-GS8F60MG56"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-GS8F60MG56'); </script>  <script async src="https://www.googletagmanager.com/gtag/js?id=UA-165638318-1"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-165638318-1'); </script> </body> </html>