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@sanger-pathogens

Pathogen Informatics, Wellcome Sanger Institute

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  1. gemsweep gemsweep Public

    Nextflow pipeline for deconvoluting mixed sample reads into bins with strain-level resolution.

    Python 7

  2. trepogeno trepogeno Public

    trepogeno is a molecular typing scheme and tool for classifying Treponema pallidum genomic data

    Python 1

Repositories

Showing 10 of 121 repositories
  • assorted-sub-workflows Public
    sanger-pathogens/assorted-sub-workflows's past year of commit activity
    Nextflow 0 AGPL-3.0 1 0 1 Updated Oct 2, 2026
  • metawrap_qc_nextflow Public
    sanger-pathogens/metawrap_qc_nextflow's past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 29, 2026
  • LSMD Public
    sanger-pathogens/LSMD's past year of commit activity
    0 MIT 0 0 0 Updated Sep 29, 2026
  • dlh-in-a-box-umbrella-helm-chart Public

    An Open Source Data Lakehouse Umbrella Helm Chart, dependent on trino, prefect, minio, hive and datahub

    sanger-pathogens/dlh-in-a-box-umbrella-helm-chart's past year of commit activity
    JavaScript 2 1 5 5 Updated Sep 27, 2026
  • strain_mapper Public
    sanger-pathogens/strain_mapper's past year of commit activity
    Python 0 0 0 0 Updated Sep 27, 2026
  • qc-short-read Public

    QC-short-read is a Nextflow DSL2 pipeline for quality control and taxonomic profiling of short-read Illumina sequencing data. It accepts data from multiple input sources and produces per-sample FastQC reports, Kraken2/Bracken taxonomic profiles, and an aggregated MultiQC summary.

    sanger-pathogens/qc-short-read's past year of commit activity
    0 MIT 0 0 0 Updated Sep 25, 2026
  • nextflowtool Public
    sanger-pathogens/nextflowtool's past year of commit activity
    Groovy 0 AGPL-3.0 1 0 0 Updated Sep 24, 2026
  • gps-pipeline-sanger Public Forked from GlobalPneumoSeq/gps-pipeline

    Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequencing Project)

    sanger-pathogens/gps-pipeline-sanger's past year of commit activity
    Nextflow 0 GPL-3.0 14 0 0 Updated Sep 23, 2026
  • gemsweep Public

    Nextflow pipeline for deconvoluting mixed sample reads into bins with strain-level resolution.

    sanger-pathogens/gemsweep's past year of commit activity
    Python 7 MIT 0 0 0 Updated Sep 19, 2026
  • rvi-viral-lens Public
    sanger-pathogens/rvi-viral-lens's past year of commit activity
    Nextflow 0 0 0 0 Updated Sep 18, 2026
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