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    6 repositories

    • MTBseq_source

      Public
      MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.
      pipelinegenomicsngsvariantsepidemiologyphylogenytuberculosismycobacterium-tuberculosis
      Perl
      •
      Other
      •23•41•7•0•Updated Aug 9, 2024Aug 9, 2024

    • NTMtools

      Public
      This repository contains scripts and manuals for whole genome sequencing based analysis of Non-tuberculous mycobacteria. Questions? Ask [email protected]
      Shell
      •1•1•0•0•Updated May 23, 2024May 23, 2024

    • HaemoSeq

      Public
      A collection of bash starter scripts and curated reference databases for the whole genome sequencing based analysis of human-related Haemophilus isolates.
      Shell
      •1•5•0•0•Updated May 21, 2024May 21, 2024

    • SARSCOV2seq

      Public
      Pipeline for the analysis of SARS-CoV-2 tiled amplicon sequencing data
      Perl
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 8, 2023Dec 8, 2023

    • binoSNP

      Public
      🔍 💊 Detection of low-frequency SNPs in next-generation sequencing data of Mycobacterium tuberculosis complex strains
      ngsresistancevariantstuberculosislow-frequency-variants
      Perl
      •
      GNU General Public License v3.0
      •1•1•1•0•Updated Feb 12, 2020Feb 12, 2020

    • SMaltophilia_phylo

      Public
      Scripts used in the The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia paper
      R
      •1•1•1•0•Updated Dec 18, 2019Dec 18, 2019