Pinned

1. phac-nml/sistr_cmd Public

   SISTR (Salmonella In Silico Typing Resource) command-line tool

   Python 14 9

2. phac-nml/biohansel Public

   Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes

   Python 24 7

3. filter_classified_reads Public

   Filter for reads from taxa of interest using Kraken2/Centrifuge classification results.

   Python 5 1

4. nf-illmap Public

   Nextflow workflow for Illumina read mapping, variant calling and consensus sequence generation using Snippy

   Nextflow 1 1

5. nf-villumina Public

   Generic viral Illumina sequence analysis pipeline

   Nextflow 1 2

6. nf-virontus Public

   Oxford Nanopore reference mapping, taxonomic classification, de novo assembly workflow primarily for viral sequence data

   Nextflow 3 1