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    43 repositories

    • sequana-wrappers

      Public
      The Sequana Wrapper Repository is a collection of reusable wrappers used in Sequana Pipelines.
      CAP CDS
      •
      BSD 3-Clause "New" or "Revised" License
      •3•1•9•0•Updated Apr 1, 2026Apr 1, 2026

    • sequana.github.io

      Public
      resource for the website
      JavaScript
      •0•0•0•0•Updated Apr 1, 2026Apr 1, 2026

    • denovo

      Public
      Denovo Assembly from FASTQ files
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Apr 1, 2026Apr 1, 2026

    • chipseq

      Public
      ChIP-seq pipeline
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•3•0•Updated Apr 1, 2026Apr 1, 2026

    • idr

      Public
      IDR
      Python
      •
      GNU General Public License v2.0
      •46•0•0•0•Updated Apr 1, 2026Apr 1, 2026

    • depletion

      Public
      Deplete Fastq files from human or other content
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•0•0•Updated Apr 1, 2026Apr 1, 2026

    • bioconvert

      Public
      convert files from one format to another using bioconvert
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Mar 31, 2026Mar 31, 2026

    • lora

      Public
      Run assembler (Canu, flye, hifiasm) on a set of long read files
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•5•13•0•Updated Mar 30, 2026Mar 30, 2026

    • sequana

      Public
      Sequana: a set of Snakemake NGS pipelines
      coveragerna-seqsnakemake
      coveragerna-seqsnakemaketaxonomyngspacbiovariant-callingde-novosequanix
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •27•151•6•0•Updated Mar 29, 2026Mar 29, 2026

    • versionix

      Public
      Versionix is a lightweight tool designed to display the version of standalone software directly on the screen, handling various versioning formats.
      parsingversioningversion
      parsingversioningversion
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•0•0•Updated Mar 28, 2026Mar 28, 2026

    • lora-demo

      Public
      a demo of sequana-lora HTML outputs
      HTML
      •0•0•0•0•Updated Mar 27, 2026Mar 27, 2026

    • sequana_pipetools

      Public
      A set of tools to help building or using sequana pipelines
      ngssequana
      ngssequana
      Python
      •3•2•0•0•Updated Mar 27, 2026Mar 27, 2026

    • demultiplex

      Public
      Sequana demultiplexing pipeline
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•5•0•0•Updated Mar 24, 2026Mar 24, 2026

    • multicov

      Public
      Snakemake pipeline wrapping sequana_coverage to analyse several samples at the same time
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Mar 21, 2026Mar 21, 2026

    • mapper

      Public
      Pipeline to map a set of FastQ files
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•2•0•Updated Mar 20, 2026Mar 20, 2026

    • sequana_pipeline_template

      Public
      a cookiecutter sequana pipeline template
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Mar 20, 2026Mar 20, 2026

    • sequanix

      Public
      Sequanix is a graphical user interface (GUI) that can be used to run Snakemake workflows.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•9•3•1•Updated Mar 5, 2026Mar 5, 2026

    • fastqc

      Public
      sequana pipeline to perform parallel fastqc and summarize results with multiqc plot
      snakemakengsfastqc
      snakemakengsfastqcsequana
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•5•0•0•Updated Mar 5, 2026Mar 5, 2026

    • multitax

      Public
      multiple taxonomic analysis using sequana_taxonomy standalone
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•1•0•Updated Jan 15, 2026Jan 15, 2026

    • ripseq

      Public
      RIP-seq analysis pipeline
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jan 14, 2026Jan 14, 2026

    • rnaseq

      Public
      RNA-seq, QC and differential analysis pipeline
      workflowrna-seqpipeline
      workflowrna-seqpipelinengsdifferential-analysissequana
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •4•17•4•0•Updated Nov 25, 2025Nov 25, 2025

    • sequana-wrappers-lite

      Public
      a light version of sequana-wrappers repository
      Python
      •0•0•0•0•Updated Nov 16, 2025Nov 16, 2025

    • variant_calling

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•6•0•Updated Nov 6, 2025Nov 6, 2025

    • ribofinder

      Public
      Workflow to find ribosomal feature in set of FastQ files
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•1•0•Updated Oct 16, 2025Oct 16, 2025

    • data

      Public
      Set of large static data files to be used for testing within Sequana
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 4, 2025Apr 4, 2025

    • hic

      Public
      Hi-C pipeline to capture 3D chromatim interactions in a genome
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Feb 8, 2025Feb 8, 2025

    • webapp_samplesheet

      Public
      test st
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•1•Updated Oct 24, 2024Oct 24, 2024

    • revcomp

      Public
      A simple utility to convert a bunch of input fastq files into their reverse complement
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•5•Updated Apr 3, 2024Apr 3, 2024

    • 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 …
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•5•Updated Apr 3, 2024Apr 3, 2024

    • GNFish

      Public
      Suite of Python programs for Gene extraction and Phylogentic Inference
      Python
      •
      GNU General Public License v3.0
      •2•0•0•1•Updated Mar 18, 2024Mar 18, 2024
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