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CompassCompact
A compact version of Oxford Compass (Complete Pathogen Analysis Software Solution)gnomonicus
Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variantstuberculosis_amr_catalogues
gumpy
Genetics with numpypiezo
SARS-CoV2_workflows
grumpy
Re-implementation of gumpy in rust for speedGenomicDiversityPaper
Scripts for "Genomic diversity affects the accuracy of bacterial SNP calling pipelines"testdata-catalog
Reposity to keep the catalog of samples for testingFN5
SNP matrix generation with caching to disk to allow fast reloadingcatsup
pre-processing and upload module for SP3AMR-catalogue-demo
A Jupyter notebook to demonstrate usage of piezo, gumpy and gnomonicus with different AMR cataloguescatsgo
Command client of SP3 for fetch, run and download.fn5_pipeline
Nextflow wrapper for FN5tb-predict-pipeline
Nextflow pipeline for producing variants, mutations and effects of a specified (minos) VCF fileflye_medaka_workflow
Bugflow_DSL2
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