Skip to content
@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.

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 tests, 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

  1. sequana Public

    Sequana: a set of Snakemake NGS pipelines

    Jupyter Notebook 112 27

  2. rnaseq Public

    RNA-seq, QC and differential analysis pipeline

    R 9 4

  3. mapper Public

    Pipeline to map a set of FastQ files

    Python 4 2

  4. demultiplex Public

    Sequana demultiplexing pipeline

    Python 3 3

  5. fastqc Public

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

    Python 2 3

  6. MergeGI Public

    Python 2 1

Repositories

  • mapper Public

    Pipeline to map a set of FastQ files

    Python 4 BSD-3-Clause 2 0 0 Updated Jun 28, 2022
  • sequana Public

    Sequana: a set of Snakemake NGS pipelines

    Jupyter Notebook 112 BSD-3-Clause 27 12 1 Updated Jun 28, 2022
  • rnaseq Public

    RNA-seq, QC and differential analysis pipeline

    R 9 BSD-3-Clause 4 3 1 Updated Jun 28, 2022
  • sequana-wrappers Public

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

    Pep8 0 BSD-3-Clause 3 3 0 Updated Apr 19, 2022
  • bioconvert Public

    convert files from one format to another using bioconvert

    Python 0 BSD-3-Clause 0 0 0 Updated Apr 12, 2022
  • sequana_pipeline_template Public

    a cookiecutter sequana pipeline template

    Python 0 BSD-3-Clause 2 0 0 Updated Apr 7, 2022
  • .github Public
    0 0 0 0 Updated Apr 6, 2022
  • sequana_pipetools Public

    A set of tools to help building or using sequana pipelines

    Python 1 3 0 0 Updated Apr 6, 2022
  • depletion Public

    Deplete Fastq files from human or other content

    Python 0 BSD-3-Clause 0 0 0 Updated Apr 1, 2022
  • quality_control Public

    A quality control pipeline for illumina data set. This pipeline removes contaminants (e.g. Phix), performs fastqc, adapter cleaning and trimming and checks for contaminants

    Python 0 BSD-3-Clause 1 0 0 Updated Mar 16, 2022
View all repositories

People

This organization has no public members. You must be a member to see who’s a part of this organization.

Top languages

Loading…

Most used topics

Loading…