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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>.</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>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> 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>

  

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