pathogen topic
Roary
Rapid large-scale prokaryote pan genome analysis
snp-sites
Finds SNP sites from a multi-FASTA alignment file
Artemis
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
circlator
A tool to circularize genome assemblies
ariba
Antimicrobial Resistance Identification By Assembly
assembly-stats
Get assembly statistics from FASTA and FASTQ files
gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Fastaq
Python3 scripts to manipulate FASTA and FASTQ files
pathogen-informatics-training