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    46 repositories

    • 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•7•0•Updated Aug 27, 2026Aug 27, 2026

    • rnaseq

      Public
      RNA-seq, QC and differential analysis pipeline
      workflowrna-seqpipeline
      workflowrna-seqpipelinengsdifferential-analysissequana
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•17•3•0•Updated Aug 27, 2026Aug 27, 2026

    • laa

      Public
      Pacbio amplicon, sequana, phylogeny, variant
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Aug 24, 2026Aug 24, 2026

    • 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•0•Updated Aug 24, 2026Aug 24, 2026

    • damona-containers

      Public
      example of alternate damona mirrors
      0•0•0•0•Updated Aug 20, 2026Aug 20, 2026

    • webapp_samplesheet

      Public
      test st
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•1•Updated Aug 17, 2026Aug 17, 2026

    • webapp_kozak

      Public
      webapp to create meme of kozak sequences
      Jupyter Notebook
      •0•0•3•0•Updated Jul 24, 2026Jul 24, 2026

    • variant_calling

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•6•0•Updated Jul 23, 2026Jul 23, 2026

    • 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 Jun 9, 2026Jun 9, 2026

    • mapper

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

    • multitax

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

    • 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 Jun 1, 2026Jun 1, 2026

    • sequana_pipetools

      Public
      A set of tools to help building or using sequana pipelines
      ngssequana
      ngssequana
      Python
      •3•2•0•0•Updated May 21, 2026May 21, 2026

    • 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 May 1, 2026May 1, 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 May 1, 2026May 1, 2026

    • bioconvert

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

    • pacbio_qc

      Public
      QC on pacbio data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•1•0•Updated Apr 17, 2026Apr 17, 2026

    • nanomerge

      Public
      Pipeline utility to perform merge of barcoded nanopore runs
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•2•0•0•Updated Apr 15, 2026Apr 15, 2026

    • 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•0•Updated Apr 14, 2026Apr 14, 2026

    • downsampling

      Public
      down sample NGS data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Apr 13, 2026Apr 13, 2026

    • chipseq

      Public
      ChIP-seq pipeline
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•3•0•Updated Apr 12, 2026Apr 12, 2026

    • denovo

      Public
      Denovo Assembly from FASTQ files
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Apr 10, 2026Apr 10, 2026

    • sequana.github.io

      Public
      resource for the website
      JavaScript
      •0•0•0•0•Updated Apr 9, 2026Apr 9, 2026

    • trf

      Public
      parallell version of trf
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Apr 7, 2026Apr 7, 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 7, 2026Apr 7, 2026

    • demultiplex

      Public
      Sequana demultiplexing pipeline
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•5•0•0•Updated Apr 7, 2026Apr 7, 2026

    • idr

      Public
      IDR
      Python
      •
      GNU General Public License v2.0
      •48•0•0•0•Updated 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
      •2•5•13•0•Updated 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.
      parsingversioningversion
      parsingversioningversion
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•1•0•Updated Mar 28, 2026Mar 28, 2026
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