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    39 repositories

    • sequana

      Public
      Sequana: a set of Snakemake NGS pipelines
      coveragerna-seqsnakemaketaxonomyngspacbiovariant-callingde-novosequanix
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •28•148•7•0•Updated Oct 16, 2025Oct 16, 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

    • rnaseq

      Public
      RNA-seq, QC and differential analysis pipeline
      workflowrna-seqpipelinengsdifferential-analysissequana
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •4•17•5•0•Updated Oct 8, 2025Oct 8, 2025

    • lora

      Public
      Run assembler (Canu, flye, hifiasm) on a set of long read files
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•5•0•Updated Sep 11, 2025Sep 11, 2025

    • versionix

      Public
      Versionix is a lightweight tool designed to display the version of standalone software directly on the screen, handling various versioning formats.
      parsingversioningversion
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•1•0•Updated Sep 5, 2025Sep 5, 2025

    • sequana_pipetools

      Public
      A set of tools to help building or using sequana pipelines
      ngssequana
      Python
      •3•2•1•0•Updated Sep 2, 2025Sep 2, 2025

    • sequana-wrappers-lite

      Public
      a light version of sequana-wrappers repository
      Python
      •0•0•0•0•Updated Jul 22, 2025Jul 22, 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

    • variant_calling

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•9•0•Updated Feb 28, 2025Feb 28, 2025

    • hic

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

    • fastqc

      Public
      sequana pipeline to perform parallel fastqc and summarize results with multiqc plot
      snakemakengsfastqcsequana
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•5•0•2•Updated Jan 8, 2025Jan 8, 2025

    • mapper

      Public
      Pipeline to map a set of FastQ files
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•2•0•Updated Nov 22, 2024Nov 22, 2024

    • webapp_samplesheet

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

    • 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•0•9•1•Updated Aug 29, 2024Aug 29, 2024

    • sequana.github.io

      Public
      resource for the website
      JavaScript
      •0•0•0•0•Updated Aug 22, 2024Aug 22, 2024

    • sequana_pipeline_template

      Public
      a cookiecutter sequana pipeline template
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Aug 8, 2024Aug 8, 2024

    • depletion

      Public
      Deplete Fastq files from human or other content
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•1•1•Updated May 22, 2024May 22, 2024

    • bioconvert

      Public
      convert files from one format to another using bioconvert
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•6•Updated Apr 3, 2024Apr 3, 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 contaminants
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•5•Updated Apr 3, 2024Apr 3, 2024

    • denovo

      Public
      Denovo Assembly from FASTQ files
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•2•0•Updated Mar 25, 2024Mar 25, 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

    • webapp_rnadiff

      Public
      Python
      •1•0•0•0•Updated Feb 21, 2024Feb 21, 2024

    • 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
      •2•8•3•0•Updated Feb 20, 2024Feb 20, 2024

    • demultiplex

      Public
      Sequana demultiplexing pipeline
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•5•2•0•Updated Dec 29, 2023Dec 29, 2023

    • downsampling

      Public
      down sample NGS data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Dec 20, 2023Dec 20, 2023

    • nanomerge

      Public
      Pipeline utility to perform merge of barcoded nanopore runs
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•2•0•0•Updated Dec 20, 2023Dec 20, 2023

    • laa

      Public
      Pacbio amplicon, sequana, phylogeny, variant
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Dec 19, 2023Dec 19, 2023

    • resources

      Public
      Set of data and resources
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 6, 2023Dec 6, 2023

    • pacbio_qc

      Public
      QC on pacbio data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•1•0•Updated Jul 7, 2023Jul 7, 2023