Pathogen Informatics, Wellcome Sanger Institute

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Hinxton, Cambs., UK
http://www.sanger.ac.uk/science/groups/pathogen-informatics

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gemsweep gemsweep Public

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

Python 4
trepogeno trepogeno Public

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

Python 1

Repositories

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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 4 Updated Aug 28, 2026
assorted-sub-workflows Public

sanger-pathogens/assorted-sub-workflows's past year of commit activity

Nextflow 0 AGPL-3.0 1 0 1 Updated Aug 28, 2026
Multiple-mappings-to-bam Public
A GSoC project - Nextflow pipeline updating the legacy Python2 Multiple mappings to bam to nextflow.

sanger-pathogens/Multiple-mappings-to-bam's past year of commit activity

Python 4 AGPL-3.0 2 1 0 Updated Aug 28, 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 4 MIT 0 0 0 Updated Aug 26, 2026
nextflowtool Public

sanger-pathogens/nextflowtool's past year of commit activity

Groovy 0 AGPL-3.0 1 0 0 Updated Aug 20, 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 0 0 Updated Aug 18, 2026
prefector Public
Prefector is a CI-first CLI helper tool for managing Prefect resources as code.

sanger-pathogens/prefector's past year of commit activity

Python 2 0 0 0 Updated Aug 12, 2026
rvi-vl-kraken-prep Public

sanger-pathogens/rvi-vl-kraken-prep's past year of commit activity

Python 0 0 0 0 Updated Aug 6, 2026
mapping-helminth Public
A pipeline for mapping helminth genomes minimap2 as a mapper and GATK/Samtools/Sambamba for further processing.

sanger-pathogens/mapping-helminth's past year of commit activity

Nextflow 0 0 0 0 Updated Aug 3, 2026
lung-microbiome-visium Public
Tool to design probes under various constraints (primarily for use with 10X Genomics Visium Spatial Gene Expression).

sanger-pathogens/lung-microbiome-visium's past year of commit activity

Python 0 0 0 0 Updated Jul 31, 2026