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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 30, 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 Oct 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 6 Updated Oct 29, 2026
  • nextflowtool Public
    sanger-pathogens/nextflowtool's past year of commit activity
    Groovy 0 AGPL-3.0 1 0 0 Updated Oct 29, 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 Oct 22, 2026
  • nextflow-commons Public

    Store of generic templates and scripts for nextflow pipelines

    sanger-pathogens/nextflow-commons's past year of commit activity
    Nextflow 1 AGPL-3.0 0 0 3 Updated Oct 21, 2026
  • qc_mags Public

    QC pipeline for Metagenome Assembled Genomes (MAGs)

    sanger-pathogens/qc_mags's past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Oct 16, 2026
  • mags_maker Public

    Generate Metagenome-Assembled Genomes (MAGs) from short-read metagenomic sequencing data. A re-implementation of generate_mags.

    sanger-pathogens/mags_maker's past year of commit activity
    Nextflow 1 MIT 0 0 0 Updated Oct 15, 2026
  • trepogeno Public

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

    sanger-pathogens/trepogeno's past year of commit activity
    Python 1 MIT 0 1 0 Updated Oct 13, 2026
  • strain_mapper Public
    sanger-pathogens/strain_mapper's past year of commit activity
    Python 0 MIT 0 0 0 Updated Oct 9, 2026
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