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    37 repositories

    • fastqc

      Public
      sequana pipeline to perform parallel fastqc and summarize results with multiqc plot
      snakemakengsfastqcsequana
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•3•0•0•Updated Oct 31, 2024Oct 31, 2024

    • sequana_pipetools

      Public
      A set of tools to help building or using sequana pipelines
      ngssequana
      Python
      •3•2•1•0•Updated Oct 31, 2024Oct 31, 2024

    • webapp_samplesheet

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

    • mapper

      Public
      Pipeline to map a set of FastQ files
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•5•2•0•Updated Oct 19, 2024Oct 19, 2024

    • rnaseq

      Public
      RNA-seq, QC and differential analysis pipeline
      workflowrna-seqpipelinengsdifferential-analysissequana
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •4•17•4•0•Updated Oct 17, 2024Oct 17, 2024

    • sequana

      Public
      Sequana: a set of Snakemake NGS pipelines
      coveragerna-seqsnakemaketaxonomyngspacbiovariant-callingde-novosequanix
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •27•144•6•0•Updated Oct 17, 2024Oct 17, 2024

    • versionix

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•1•0•Updated Oct 10, 2024Oct 10, 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•0•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•0•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•6•3•0•Updated Feb 20, 2024Feb 20, 2024

    • variant_calling

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•5•0•Updated Jan 31, 2024Jan 31, 2024

    • demultiplex

      Public
      Sequana demultiplexing pipeline
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•4•2•0•Updated Dec 29, 2023Dec 29, 2023

    • lora

      Public
      Run assembler (Canu, flye, hifiasm) on a set of long read files
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•5•0•Updated Dec 20, 2023Dec 20, 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•1•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

    • ribofinder

      Public
      Workflow to find ribosomal feature in set of FastQ files
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Dec 5, 2023Dec 5, 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

    • multicov

      Public
      Snakemake pipeline wrapping sequana_coverage to analyse several samples at the same time
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•1•0•Updated May 23, 2023May 23, 2023

    • circlator

      Public
      A tool to circularize genome assemblies
      Python
      •
      Other
      •60•0•0•0•Updated Mar 24, 2023Mar 24, 2023

    • MergeGI

      Public
      MergeGI provides a single command line to merge and select barcoded raw data from MGI sequencing runs into a set of FastQ files ready for subsequent bioinformatics analysis.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•2•0•Updated Jan 10, 2023Jan 10, 2023