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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 variantsgumpy
Genetics with numpytuberculosis_amr_catalogues
piezo
SARS-CoV2_workflows
grumpy
Re-implementation of gumpy in rust for speedGenomicDiversityPaper
Scripts for "Genomic diversity affects the accuracy of bacterial SNP calling pipelines"FN5
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 cataloguesspeciation
Scripts for Mycobacterium Speciationcatsgo
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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