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    • hic

      Public
      Hi-C pipeline to capture 3D chromatim interactions in a genome
      Python
      BSD 3-Clause "New" or "Revised" License
      1000Updated Apr 11, 2026Apr 11, 2026
    • multitax

      Public
      multiple taxonomic analysis using sequana_taxonomy standalone
      Python
      BSD 3-Clause "New" or "Revised" License
      1210Updated Apr 10, 2026Apr 10, 2026
    • denovo

      Public
      Denovo Assembly from FASTQ files
      Python
      BSD 3-Clause "New" or "Revised" License
      2000Updated Apr 10, 2026Apr 10, 2026
    • sequana_pipetools

      Public
      A set of tools to help building or using sequana pipelines
      Python
      3200Updated Apr 10, 2026Apr 10, 2026
    • ribofinder

      Public
      Workflow to find ribosomal feature in set of FastQ files
      Python
      BSD 3-Clause "New" or "Revised" License
      2010Updated Apr 9, 2026Apr 9, 2026
    • sequana.github.io

      Public
      resource for the website
      JavaScript
      0000Updated Apr 9, 2026Apr 9, 2026
    • variant_calling

      Public
      Python
      BSD 3-Clause "New" or "Revised" License
      3060Updated Apr 8, 2026Apr 8, 2026
    • multicov

      Public
      Snakemake pipeline wrapping sequana_coverage to analyse several samples at the same time
      Python
      BSD 3-Clause "New" or "Revised" License
      1100Updated Apr 8, 2026Apr 8, 2026
    • trf

      Public
      parallell version of trf
      Python
      BSD 3-Clause "New" or "Revised" License
      1000Updated Apr 7, 2026Apr 7, 2026
    • rnaseq

      Public
      RNA-seq, QC and differential analysis pipeline
      R
      BSD 3-Clause "New" or "Revised" License
      41740Updated Apr 7, 2026Apr 7, 2026
    • sequana

      Public
      Sequana: a set of Snakemake NGS pipelines
      Python
      BSD 3-Clause "New" or "Revised" License
      2715170Updated Apr 7, 2026Apr 7, 2026
    • depletion

      Public
      Deplete Fastq files from human or other content
      Python
      BSD 3-Clause "New" or "Revised" License
      2100Updated Apr 7, 2026Apr 7, 2026
    • mapper

      Public
      Pipeline to map a set of FastQ files
      Python
      BSD 3-Clause "New" or "Revised" License
      2420Updated Apr 7, 2026Apr 7, 2026
    • fastqc

      Public
      sequana pipeline to perform parallel fastqc and summarize results with multiqc plot
      Python
      BSD 3-Clause "New" or "Revised" License
      3500Updated Apr 7, 2026Apr 7, 2026
    • The Sequana Wrapper Repository is a collection of reusable wrappers used in Sequana Pipelines.
      CAP CDS
      BSD 3-Clause "New" or "Revised" License
      3190Updated Apr 7, 2026Apr 7, 2026
    • Sequana demultiplexing pipeline
      Python
      BSD 3-Clause "New" or "Revised" License
      3500Updated Apr 7, 2026Apr 7, 2026
    • convert files from one format to another using bioconvert
      Python
      BSD 3-Clause "New" or "Revised" License
      1100Updated Apr 7, 2026Apr 7, 2026
    • idr

      Public
      IDR
      Python
      GNU General Public License v2.0
      46000Updated Apr 3, 2026Apr 3, 2026
    • chipseq

      Public
      ChIP-seq pipeline
      Python
      BSD 3-Clause "New" or "Revised" License
      1031Updated Apr 3, 2026Apr 3, 2026
    • lora

      Public
      Run assembler (Canu, flye, hifiasm) on a set of long read files
      Python
      BSD 3-Clause "New" or "Revised" License
      25130Updated Mar 30, 2026Mar 30, 2026
    • versionix

      Public
      Versionix is a lightweight tool designed to display the version of standalone software directly on the screen, handling various versioning formats.
      Python
      BSD 3-Clause "New" or "Revised" License
      3000Updated Mar 28, 2026Mar 28, 2026
    • lora-demo

      Public
      a demo of sequana-lora HTML outputs
      HTML
      0000Updated Mar 27, 2026Mar 27, 2026
    • a cookiecutter sequana pipeline template
      Python
      BSD 3-Clause "New" or "Revised" License
      2000Updated 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
      1931Updated Mar 5, 2026Mar 5, 2026
    • ripseq

      Public
      RIP-seq analysis pipeline
      Python
      BSD 3-Clause "New" or "Revised" License
      1000Updated Jan 14, 2026Jan 14, 2026
    • a light version of sequana-wrappers repository
      Python
      0000Updated Nov 16, 2025Nov 16, 2025
    • data

      Public
      Set of large static data files to be used for testing within Sequana
      BSD 3-Clause "New" or "Revised" License
      0000Updated Apr 4, 2025Apr 4, 2025
    • test st
      Python
      BSD 3-Clause "New" or "Revised" License
      1301Updated 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
      1005Updated Apr 3, 2024Apr 3, 2024
    • 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
      1105Updated Apr 3, 2024Apr 3, 2024
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