Software used in this pipeline
We gratefully acknowledge the trememdous efforts put in by many developers without whose work GABI would not exist. For a list of packages used in this pipeline, please see the (hopefully comprehensive) list below. For the very latest versions and tools used, please consult the pipeline report.
Abricate Version 1.0.1, github
AMRfinder Plus Version 3.11.18, doi | PubMed | github
Autocycler Version 0.5.2, doi | PubMed | github
Bracken Version 2.9, github
BTyper3 Version 3.4.0, doi, Pubmed, github
Busco Version 5.3.0, doi | PubMed | Website
BWAMEM 2 Version 2.2.1, doi | github | IEEE Explore
ConfindR Version 0.7.4, doi | PubMed | github
DNAAPLER Version 1.1.0, github
ECTyper Version 2.0.0, github
FastP Version 0.24, doi | PubMed | github
FastPlong Version 0.4.1, doi | PubMed | github
Flye Version 2.9, doi | PubMed | github
Hamronization Version 1.1.4, github
Homopolish Version 0.4.1, doi | PubMed | github
Kaptive Version 3.1.0, doi | PubMed | github
Lissero Version 0.4.9, github
Kraken2 Version 2.1.2, doi | PubMed | github
Medaka Version 2.0.1, github
Minimap2 Version 2.28, doi | PubMed | github
MLST Version 2.23.0, github
Mob Suite Version 3.1.8, doi | PubMed | github
MultiQC Version 1.19, doi | PubMed | github
Mosdepth Version 0.3.8, github
Quast Version 5.2.0, github
Racon Version 1.4.3, doi | PubMed | github
Polypolish Version 0.6.0, doi | PubMed | github
Porechop_abi Version 0.5.0, doi | BiorXiv | github
Prokka Version 1.14.6, doi | PubMed | github
Samtools Version 1.19, doi | PubMed | github
SeqSero2 Version 1.3.1, doi, PubMed, github
Shovill Version 1.1.0, github
Sistr Version 1.1.1, github
Sccmec Version 1.2.0 github
Snippy Version 4.6.0, github
Sourmash Version 4.8.4, github
Stecfinder Version 1.1.0, github