Bakta

Prokka: rapid prokaryotic genome annotation. Prokka is one of the most cited annotation command line tools for microbial genome annotations.

JavaScript genome browser that is highly customizable via plugins and track customizations.

Annotate a VCF with other VCFs/BEDs/tabixed files.

Pairwise SNP distance matrix from a FASTA sequence alignment

UNIX-style FASTA manipulation tools.

AcinetoScope is an automated, comprehensive bioinformatics pipeline designed specifically for the genomic analysis of Acinetobacter baumannii, a WHO Critical Priority pathogen responsible for devastating hospital-acquired infections. It integrates seven analysis types (MLST, ABRicate, AMRFinder, Kaptive 3, APT, PlasmidFinder, and mutation detection) into a single automated workflow — from FASTA to actionable insights. The pipeline offers both gene-centric and sample-centric reporting, dynamic grouping by typing, and is optimised for HPC, cloud, and container environments.