index.html

---
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title: Sequana Project
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---
<div class="blurb">
	<h1>Sequana: a set of NGS pipelines</h1>
	<p>This page serves as an additional set of resources for
		the Sequana project. Sequana is comprised of a Python library, the
        documentation of which is accessible on <a href="http://sequana.readthedocs.org">Read The Docs</a>.
        The source code for the Python library can be found on
		<a href="http://github.com/sequana/sequana">GitHub</a>.
        If you use Sequana, please cite: Cokelaer <em>et al.</em>,
        <em>Journal of Open Source Software</em>, 2017
        (<a href="https://doi.org/10.21105/joss.00352" target="_blank" rel="noopener noreferrer">doi:10.21105/joss.00352</a>).
        &nbsp;
        <a href="https://doi.org/10.21105/joss.00352" target="_blank" rel="noopener noreferrer">
          <img src="https://joss.theoj.org/papers/10.21105/joss.00352/status.svg"
               alt="JOSS paper" style="vertical-align:middle;"/>
        </a>
    </p>

    <p>One of the primary objective of the Sequana project is to offer a collection of NGS pipelines.
    The pipelines currently available are located on PyPI and the <a
      href="https://github.com/sequana/sequana">Sequana GitHub organisation page</a>,
   each having their own repository. For instance, the RNA-seq pipeline can be found at <a href="https://github.com/sequana/rnaseq">sequana/rnaseq</a>.

	<div>
    This page is also a place for providing supplementary information to the main repositories.
    </div>

    <h2 id="pipelines">Pipelines</h2>
    <p>Sequana provides a collection of NGS pipelines. Each pipeline lives in its own repository on the
    <a href="https://github.com/sequana">Sequana GitHub organisation</a>. Below are some highlighted pipelines:</p>

    <div class="pipeline-grid">

      <!-- sequana_fastqc -->
      <div class="pipeline-card">
        <img class="pipeline-card-image"
             src="images/pipeline_fastqc_overview.png"
             alt="sequana_fastqc pipeline overview"/>
        <div class="pipeline-card-body">
          <div class="pipeline-card-title">sequana_fastqc</div>
          <div class="pipeline-card-desc">
            A quality-control pipeline that runs FastQC and MultiQC on raw FASTQ files to assess sequencing quality.
          </div>
          <div class="pipeline-card-links">
            <a class="btn-github"
               href="https://github.com/sequana/sequana_fastqc"
               target="_blank" rel="noopener noreferrer">&#128279; GitHub</a>
            <a class="btn-docs"
               href="https://github.com/sequana/sequana_fastqc#readme"
               target="_blank" rel="noopener noreferrer">&#128214; README</a>
            <a href="https://github.com/sequana/sequana_fastqc"
               target="_blank" rel="noopener noreferrer">
              <img src="https://img.shields.io/github/stars/sequana/sequana_fastqc?style=flat&label=⭐"
                   alt="GitHub stars" style="vertical-align:middle;"/>
            </a>
            <a class="btn-report"
               href="fastqc-demo/"
               target="_blank" rel="noopener noreferrer">&#128196; Report</a>
          </div>
        </div>
      </div>

      <!-- sequana_rnaseq -->
      <div class="pipeline-card">
        <img class="pipeline-card-image"
             src="images/pipeline_rnaseq_overview.png"
             alt="sequana_rnaseq pipeline overview"/>
        <div class="pipeline-card-body">
          <div class="pipeline-card-title">sequana_rnaseq</div>
          <div class="pipeline-card-desc">
            An RNA-seq pipeline that covers trimming, alignment, feature counting, and differential expression analysis.
          </div>
          <div class="pipeline-card-links">
            <a class="btn-github"
               href="https://github.com/sequana/rnaseq"
               target="_blank" rel="noopener noreferrer">&#128279; GitHub</a>
            <a class="btn-docs"
               href="https://github.com/sequana/rnaseq#readme"
               target="_blank" rel="noopener noreferrer">&#128214; README</a>
            <a href="https://github.com/sequana/rnaseq"
               target="_blank" rel="noopener noreferrer">
              <img src="https://img.shields.io/github/stars/sequana/rnaseq?style=flat&label=⭐"
                   alt="GitHub stars" style="vertical-align:middle;"/>
            </a>
            <a class="btn-report"
               href="html_examples/rnaseq/"
               target="_blank" rel="noopener noreferrer">&#128196; Report</a>
          </div>
        </div>
      </div>

      <!-- sequana_variant_calling -->
      <div class="pipeline-card">
        <img class="pipeline-card-image"
             src="images/pipeline_variant_calling_overview.png"
             alt="sequana_variant_calling pipeline overview"/>
        <div class="pipeline-card-body">
          <div class="pipeline-card-title">sequana_variant_calling</div>
          <div class="pipeline-card-desc">
            A variant-calling pipeline that performs read trimming, alignment, and SNP/indel detection
            using standard tools such as BWA and freebayes, with interactive HTML reports.
          </div>
          <div class="pipeline-card-links">
            <a class="btn-github"
               href="https://github.com/sequana/variant_calling"
               target="_blank" rel="noopener noreferrer">&#128279; GitHub</a>
            <a class="btn-docs"
               href="https://github.com/sequana/variant_calling#readme"
               target="_blank" rel="noopener noreferrer">&#128214; README</a>
            <a href="https://github.com/sequana/variant_calling"
               target="_blank" rel="noopener noreferrer">
              <img src="https://img.shields.io/github/stars/sequana/variant_calling?style=flat&label=⭐"
                   alt="GitHub stars" style="vertical-align:middle;"/>
            </a>
            <a class="btn-report"
               href="html_examples/variant_calling/"
               target="_blank" rel="noopener noreferrer">&#128196; Report</a>
          </div>
        </div>
      </div>

      <!-- sequana_lora -->
      <div class="pipeline-card">
        <img class="pipeline-card-image"
             src="images/pipeline_lora_overview.png"
             alt="sequana_lora pipeline overview"/>
        <div class="pipeline-card-body">
          <div class="pipeline-card-title">sequana_lora</div>
          <div class="pipeline-card-desc">
            A long-read assembly pipeline for Oxford Nanopore (and PacBio) data that performs
            basecalling, quality control, de-novo assembly, polishing, and assembly quality
            assessment with tools such as Flye, Medaka, and BUSCO.
          </div>
          <div class="pipeline-card-links">
            <a class="btn-github"
               href="https://github.com/sequana/lora"
               target="_blank" rel="noopener noreferrer">&#128279; GitHub</a>
            <a class="btn-docs"
               href="https://github.com/sequana/lora#readme"
               target="_blank" rel="noopener noreferrer">&#128214; README</a>
            <a href="https://github.com/sequana/lora"
               target="_blank" rel="noopener noreferrer">
              <img src="https://img.shields.io/github/stars/sequana/lora?style=flat&label=⭐"
                   alt="GitHub stars" style="vertical-align:middle;"/>
            </a>
            <a class="btn-report"
               href="https://sequana.github.io/lora-demo"
               target="_blank" rel="noopener noreferrer">&#128196; Report</a>
          </div>
        </div>
      </div>

      <!-- sequana_multitax -->
      <div class="pipeline-card">
        <img class="pipeline-card-image"
             src="images/pipeline_multitax_overview.png"
             alt="sequana_multitax pipeline overview"/>
        <div class="pipeline-card-body">
          <div class="pipeline-card-title">sequana_multitax</div>
          <div class="pipeline-card-desc">
            A taxonomic classification pipeline that runs multiple classifiers (Kraken2, Centrifuge, etc.)
            on sequencing reads, merges results, and produces comparative summary reports.
          </div>
          <div class="pipeline-card-links">
            <a class="btn-github"
               href="https://github.com/sequana/multitax"
               target="_blank" rel="noopener noreferrer">&#128279; GitHub</a>
            <a class="btn-docs"
               href="https://github.com/sequana/multitax#readme"
               target="_blank" rel="noopener noreferrer">&#128214; README</a>
            <a href="https://github.com/sequana/multitax"
               target="_blank" rel="noopener noreferrer">
              <img src="https://img.shields.io/github/stars/sequana/multitax?style=flat&label=⭐"
                   alt="GitHub stars" style="vertical-align:middle;"/>
            </a>
          </div>
        </div>
      </div>

      <!-- sequana_demultiplex -->
      <div class="pipeline-card">
        <img class="pipeline-card-image"
             src="images/pipeline_demultiplex_overview.png"
             alt="sequana_demultiplex pipeline overview"/>
        <div class="pipeline-card-body">
          <div class="pipeline-card-title">sequana_demultiplex</div>
          <div class="pipeline-card-desc">
            A demultiplexing pipeline built around bcl2fastq / bcl-convert that converts Illumina
            BCL files into FASTQ files, validates sample sheets, and generates MultiQC summary reports.
          </div>
          <div class="pipeline-card-links">
            <a class="btn-github"
               href="https://github.com/sequana/demultiplex"
               target="_blank" rel="noopener noreferrer">&#128279; GitHub</a>
            <a class="btn-docs"
               href="https://github.com/sequana/demultiplex#readme"
               target="_blank" rel="noopener noreferrer">&#128214; README</a>
            <a href="https://github.com/sequana/demultiplex"
               target="_blank" rel="noopener noreferrer">
              <img src="https://img.shields.io/github/stars/sequana/demultiplex?style=flat&label=⭐"
                   alt="GitHub stars" style="vertical-align:middle;"/>
            </a>
            <a class="btn-report"
               href="html_examples/demultiplex/"
               target="_blank" rel="noopener noreferrer">&#128196; Report</a>
          </div>
        </div>
      </div>

      <!-- sequana_hic -->
      <div class="pipeline-card">
        <img class="pipeline-card-image"
             src="images/pipeline_hic_overview.png"
             alt="sequana_hic pipeline overview"/>
        <div class="pipeline-card-body">
          <div class="pipeline-card-title">sequana_hic</div>
          <div class="pipeline-card-desc">
            A Hi-C pipeline for chromatin conformation capture data that performs read trimming,
            alignment, contact-map generation, and quality assessment of 3D genome organisation.
          </div>
          <div class="pipeline-card-links">
            <a class="btn-github"
               href="https://github.com/sequana/hic"
               target="_blank" rel="noopener noreferrer">&#128279; GitHub</a>
            <a class="btn-docs"
               href="https://github.com/sequana/hic#readme"
               target="_blank" rel="noopener noreferrer">&#128214; README</a>
            <a href="https://github.com/sequana/hic"
               target="_blank" rel="noopener noreferrer">
              <img src="https://img.shields.io/github/stars/sequana/hic?style=flat&label=⭐"
                   alt="GitHub stars" style="vertical-align:middle;"/>
            </a>
          </div>
        </div>
      </div>

      <!-- sequana_chipseq -->
      <div class="pipeline-card">
        <img class="pipeline-card-image"
             src="images/pipeline_chipseq_overview.png"
             alt="sequana_chipseq pipeline overview"/>
        <div class="pipeline-card-body">
          <div class="pipeline-card-title">sequana_chipseq</div>
          <div class="pipeline-card-desc">
            A ChIP-seq pipeline that covers read trimming, alignment, peak calling, and
            downstream annotation to identify protein–DNA binding sites and histone modifications.
          </div>
          <div class="pipeline-card-links">
            <a class="btn-github"
               href="https://github.com/sequana/chipseq"
               target="_blank" rel="noopener noreferrer">&#128279; GitHub</a>
            <a class="btn-docs"
               href="https://github.com/sequana/chipseq#readme"
               target="_blank" rel="noopener noreferrer">&#128214; README</a>
            <a href="https://github.com/sequana/chipseq"
               target="_blank" rel="noopener noreferrer">
              <img src="https://img.shields.io/github/stars/sequana/chipseq?style=flat&label=⭐"
                   alt="GitHub stars" style="vertical-align:middle;"/>
            </a>
          </div>
        </div>
      </div>

      <!-- sequana_denovo -->
      <div class="pipeline-card">
        <img class="pipeline-card-image"
             src="images/pipeline_denovo_overview.png"
             alt="sequana_denovo pipeline overview"/>
        <div class="pipeline-card-body">
          <div class="pipeline-card-title">sequana_denovo</div>
          <div class="pipeline-card-desc">
            A de-novo assembly pipeline for short-read Illumina data that performs trimming,
            assembly, scaffolding, and assembly quality assessment with tools such as SPAdes and QUAST.
          </div>
          <div class="pipeline-card-links">
            <a class="btn-github"
               href="https://github.com/sequana/denovo"
               target="_blank" rel="noopener noreferrer">&#128279; GitHub</a>
            <a class="btn-docs"
               href="https://github.com/sequana/denovo#readme"
               target="_blank" rel="noopener noreferrer">&#128214; README</a>
            <a href="https://github.com/sequana/denovo"
               target="_blank" rel="noopener noreferrer">
              <img src="https://img.shields.io/github/stars/sequana/denovo?style=flat&label=⭐"
                   alt="GitHub stars" style="vertical-align:middle;"/>
            </a>
          </div>
        </div>
      </div>

      <!-- sequana_ribofinder -->
      <div class="pipeline-card">
        <img class="pipeline-card-image"
             src="images/pipeline_ribofinder_overview.png"
             alt="sequana_ribofinder pipeline overview"/>
        <div class="pipeline-card-body">
          <div class="pipeline-card-title">sequana_ribofinder</div>
          <div class="pipeline-card-desc">
            A pipeline that quantifies ribosomal RNA content in sequencing data by mapping reads
            against rRNA references, helping to assess rRNA contamination and depletion efficiency
            in RNA-seq experiments.
          </div>
          <div class="pipeline-card-links">
            <a class="btn-github"
               href="https://github.com/sequana/ribofinder"
               target="_blank" rel="noopener noreferrer">&#128279; GitHub</a>
            <a class="btn-docs"
               href="https://github.com/sequana/ribofinder#readme"
               target="_blank" rel="noopener noreferrer">&#128214; README</a>
            <a href="https://github.com/sequana/ribofinder"
               target="_blank" rel="noopener noreferrer">
              <img src="https://img.shields.io/github/stars/sequana/ribofinder?style=flat&label=⭐"
                   alt="GitHub stars" style="vertical-align:middle;"/>
            </a>
          </div>
        </div>
      </div>

    </div>

    <p>These are just a few highlights. Sequana encompasses many more pipelines — both public and
    private — covering a wide range of sequencing applications. A broader overview is available on
    <a href="https://github.com/sequana/sequana" target="_blank" rel="noopener noreferrer">github.com/sequana/sequana</a>,
    the <a href="https://github.com/sequana" target="_blank" rel="noopener noreferrer">Sequana GitHub organisation</a>,
    and the full documentation at
    <a href="https://sequana.readthedocs.io" target="_blank" rel="noopener noreferrer">sequana.readthedocs.io</a>.</p>

    <h2 id="tools">Tools &amp; Standalone Applications</h2>
    <p>Sequana ships published tools and a set of standalone sub-commands invocable directly from
    the command line (<code>sequana &lt;subcommand&gt;</code>), all distributed as part of the
    <a href="https://github.com/sequana/sequana">sequana Python package</a>.</p>

    <div class="tool-grid">

      <!-- Sequana Coverage -->
      <div class="tool-card">
        <img class="tool-card-image"
             src="https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/gigascience/7/12/10.1093_gigascience_giy110/2/m_gigascience_7_12_giy110_f1.jpeg?Expires=1775777202&Signature=JmOqNJn5DDFwVFAEb1uyro~2Di~vrsww5UW9Btme3k0dmN2iykH-g0C3l360WILP-glK8lRmYlezQJJQ4k-gaaHdGwr8CGWMebOrXPwSOXp~ZlR9-Rl2kHKbrJa3xrNjfChiCyEilxkB5RLP-gQ3Lumiewp0AFr84pzQFqL-avA~mUmigPlu1dsxImp6t62qnRGkL3s-zK1-UAwwJaUGls6pgy4eUiqNa0UOVoxjJuLaKTo5K0mJ1KBgrBEfImN0ROc9Vh59Q9TGwT6I0r1EMxkkgGpUUv-LS9SFar~M0rBMvXhZjA~XOirfwslTWAlSw7SiiqOODEEZrJcNNJgvRg__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA"
             alt="Sequana Coverage — genome depth-of-coverage analysis (GigaScience 2018 Fig. 1)"/>
        <div class="tool-card-body">
          <div class="tool-card-title">Sequana Coverage</div>
          <div class="tool-card-doi">
            Published in <em>GigaScience</em> &mdash;
            DOI: <a href="https://doi.org/10.1093/gigascience/giy110"
                    target="_blank" rel="noopener noreferrer">10.1093/gigascience/giy110</a>
          </div>
          <div class="tool-card-desc">
            Fast detection of genomic regions with abnormal depth of coverage. Models coverage
            with a mixture of distributions, highlights deletions, duplications, and
            low-complexity regions, and produces interactive HTML reports.
          </div>
          <div class="tool-card-links">
            <a class="btn-github"
               href="https://github.com/sequana/sequana"
               target="_blank" rel="noopener noreferrer">&#128279; GitHub</a>
            <a class="btn-docs"
               href="https://sequana.readthedocs.io/en/latest/coverage.html"
               target="_blank" rel="noopener noreferrer">&#128214; Docs</a>
          </div>
        </div>
      </div>

      <!-- Sequanix -->
      <div class="tool-card">
        <img class="tool-card-image"
             src="images/tool_sequanix.png"
             alt="Sequanix — desktop GUI for Snakemake pipelines"/>
        <div class="tool-card-body">
          <div class="tool-card-title">Sequanix</div>
          <div class="tool-card-doi">
            Published in <em>Bioinformatics</em> &mdash;
            DOI: <a href="https://doi.org/10.1093/bioinformatics/bty034"
                    target="_blank" rel="noopener noreferrer">10.1093/bioinformatics/bty034</a>
          </div>
          <div class="tool-card-desc">
            Desktop GUI (PyQt5) for configuring and executing Snakemake pipelines without writing
            code. Dynamically renders widgets from config files and monitors pipeline progress
            in real time.
          </div>
          <div class="tool-card-links">
            <a class="btn-github"
               href="https://github.com/sequana/sequana"
               target="_blank" rel="noopener noreferrer">&#128279; GitHub</a>
            <a class="btn-docs"
               href="https://sequana.readthedocs.io/en/latest/sequanix.html"
               target="_blank" rel="noopener noreferrer">&#128214; Docs</a>
          </div>
        </div>
      </div>

      <!-- sequana taxonomy subcmd -->
      <div class="tool-card tool-card--subcmd">
        <div class="tool-card-body">
          <div class="tool-card-title"><code>sequana taxonomy</code></div>
          <div class="tool-card-desc">
            Taxonomic classification of reads using Kraken2, with summary plots for
            metagenomics studies.
          </div>
          <div class="tool-card-links">
            <a class="btn-docs" href="https://sequana.readthedocs.io/en/latest/tutorial.html"
               target="_blank" rel="noopener noreferrer">&#128214; Docs</a>
          </div>
        </div>
      </div>

      <!-- sequana summary subcmd -->
      <div class="tool-card tool-card--subcmd">
        <div class="tool-card-body">
          <div class="tool-card-title"><code>sequana summary</code></div>
          <div class="tool-card-desc">
            Summary statistics (read counts, GC content, quality metrics) for FASTQ files
            without running a full pipeline.
          </div>
          <div class="tool-card-links">
            <a class="btn-docs" href="https://sequana.readthedocs.io/en/latest/applications.html"
               target="_blank" rel="noopener noreferrer">&#128214; Docs</a>
          </div>
        </div>
      </div>

      <!-- sequana enrichment subcmd -->
      <div class="tool-card tool-card--subcmd">
        <div class="tool-card-body">
          <div class="tool-card-title"><code>sequana enrichment</code></div>
          <div class="tool-card-desc">
            Gene Ontology and KEGG pathway enrichment analysis on differentially expressed
            genes, with interactive visualisations.
          </div>
          <div class="tool-card-links">
            <a class="btn-docs" href="https://sequana.readthedocs.io/en/latest/applications.html"
               target="_blank" rel="noopener noreferrer">&#128214; Docs</a>
          </div>
        </div>
      </div>

      <!-- sequana samplesheet subcmd -->
      <div class="tool-card tool-card--subcmd">
        <div class="tool-card-body">
          <div class="tool-card-title"><code>sequana samplesheet</code></div>
          <div class="tool-card-desc">
            Validate and convert Illumina sample-sheet files, catching formatting errors before
            demultiplexing.
          </div>
          <div class="tool-card-links">
            <a class="btn-docs" href="https://sequana.readthedocs.io/en/latest/applications.html"
               target="_blank" rel="noopener noreferrer">&#128214; Docs</a>
          </div>
        </div>
      </div>

      <!-- sequana gtf_fixer subcmd -->
      <div class="tool-card tool-card--subcmd">
        <div class="tool-card-body">
          <div class="tool-card-title"><code>sequana gtf_fixer</code></div>
          <div class="tool-card-desc">
            Fix common inconsistencies in GTF/GFF annotation files so they are compatible with
            downstream RNA-seq tools.
          </div>
          <div class="tool-card-links">
            <a class="btn-docs" href="https://sequana.readthedocs.io/en/latest/applications.html"
               target="_blank" rel="noopener noreferrer">&#128214; Docs</a>
          </div>
        </div>
      </div>

    </div>

    <h2 id="talks">Talks</h2>
    <div> 
        <ul>
            <li><a href="https://sequana.github.io/talks/2024_repro_IP/index.html">Sequana and Damona (Jan 2024, Institut Pasteur, Paris)</a></li>
            <li><a href="https://sequana.github.io/talks/2024_LORA_IP/index.html">LORA (March 2024, Nanopore day, Institut Pastenstitut Pasteur, Paris)</a></li>
        </ul>
    </div>

    <h2 id="applications">Web Applications</h2>

<h3> Check your Illumina Sample Sheet</h3>

 <iframe
                    loading="lazy"
                    src="https://check-my-sample-sheet.streamlit.app/?embed=true"
                    style="
                        width: 100%;
                        border: solid 2px;
                        margin-bottom: 1rem;
                        height: 450px
                    "
                    allow="camera;clipboard-read;clipboard-write;"
                ></iframe>

    <h2> Report examples (click on the image)</h2>
    The following was generated with the Sequana Coverage standalone application and keep here a it is reference in other places. This is the coverage along a virus genome where the black dot line represent the coverage, the blue is the median coverage, and red lines are the top and bottow thresholds for detecting event of interest.
    <div class="change">
        <a href="examples/coverage_virus/coverage_mapping.chrom1.html">
        <img src="images/coverage.png"></img></a>
    </div>

  

</div>