Comparisons between SRST2, ARIBA, and KmerResistance
SRST21, ARIBA2, and KmerResistance (web service, code)3 are three widely used pieces of standalone software for read-based detection of target genes in bacterial genomes. Published in 2014, SRST2 is recognised as the pioneer amongst these three tools2, 3. In this post, I compare methodologies underlying these tools in a concise manner to shed light on the selection of appropriate software for gene detection. Particularly, I herein presume that detecting antimicrobial resistance determinants is the only use case. Whenever unspecified, software versions referred to in this post are: SRST2 v0.2.0, ARIBA 2.14.4, and KmerResistance v2.2.