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@sequana

sequana

README.md

Welcome to the github page of Sequana!

We develop tools and pipelines related to NGS that are used within a Sequencing platform (https://biomics.pasteur.fr) .

Our goal is to provide easy-to-use tools to help students, postdocs, researchers to make the most of their data. Towards this goal, we wanted to integrate expert knowledge (‘omics’) knowledge into workflows based and a uniformised user interface for all workflows. To this end, we have decided to use Snakemake and Python language and developed a common toolbox, re-usable [wrappers](tools for Snakemake pipelines, and a general-purpose Python library for data analysis sequana.

Our pipelines and tools are tested, documented, validated. There are lots of tools and pipelines developed around Sequana. Please have a look here and join us. You are welcome!

Popular repositories Loading

  1. sequana sequana Public

    Sequana: a set of Snakemake NGS pipelines

    Jupyter Notebook 146 27

  2. rnaseq rnaseq Public

    RNA-seq, QC and differential analysis pipeline

    R 17 4

  3. sequanix sequanix Public

    Sequanix is a graphical user interface (GUI) that can be used to run Snakemake workflows.

    Python 6 2

  4. mapper mapper Public

    Pipeline to map a set of FastQ files

    Python 5 2

  5. demultiplex demultiplex Public

    Sequana demultiplexing pipeline

    Python 4 3

  6. fastqc fastqc Public

    sequana pipeline to perform parallel fastqc and summarize results with multiqc plot

    Python 3 3

Repositories

Showing 10 of 37 repositories
  • mapper Public

    Pipeline to map a set of FastQ files

    sequana/mapper’s past year of commit activity
    Python 5 BSD-3-Clause 2 2 0 Updated Nov 22, 2024
  • sequana_pipetools Public

    A set of tools to help building or using sequana pipelines

    sequana/sequana_pipetools’s past year of commit activity
    Python 2 3 1 0 Updated Nov 21, 2024
  • fastqc Public

    sequana pipeline to perform parallel fastqc and summarize results with multiqc plot

    sequana/fastqc’s past year of commit activity
    Python 3 BSD-3-Clause 3 0 1 Updated Nov 18, 2024
  • webapp_samplesheet Public

    test st

    sequana/webapp_samplesheet’s past year of commit activity
    Python 3 BSD-3-Clause 0 0 0 Updated Oct 24, 2024
  • rnaseq Public

    RNA-seq, QC and differential analysis pipeline

    sequana/rnaseq’s past year of commit activity
    R 17 BSD-3-Clause 4 4 0 Updated Oct 17, 2024
  • sequana Public

    Sequana: a set of Snakemake NGS pipelines

    sequana/sequana’s past year of commit activity
    Jupyter Notebook 146 BSD-3-Clause 27 6 0 Updated Oct 17, 2024
  • versionix Public
    sequana/versionix’s past year of commit activity
    Python 0 BSD-3-Clause 3 1 0 Updated Oct 10, 2024
  • sequana-wrappers Public

    The Sequana Wrapper Repository is a collection of reusable wrappers used in Sequana Pipelines.

    sequana/sequana-wrappers’s past year of commit activity
    CAP CDS 0 BSD-3-Clause 3 9 0 Updated Aug 29, 2024
  • sequana.github.io Public

    resource for the website

    sequana/sequana.github.io’s past year of commit activity
    JavaScript 0 0 0 0 Updated Aug 22, 2024
  • sequana_pipeline_template Public

    a cookiecutter sequana pipeline template

    sequana/sequana_pipeline_template’s past year of commit activity
    Python 0 BSD-3-Clause 2 0 0 Updated Aug 8, 2024
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