Please note that this version of kairos is indefinitely shuttered and not under active development. A new version with a unique git will be released in the near future.
Kairos is a nextflow pipeline for detecting horizontal gene transfer, distinguishing misassemblies from genuine structural variation, and inferring in situ horizontal gene transfer from metagenomes and assemblies. At present, it has two workflows:
kairos derep-detect: predicts putative HGTs given contigs, contig taxonomy, an MGE database, and a target gene database
kairos assess: sensitively detects the presence of a set of given contigs within user provided samples -- sensitive to microdiversity-level differences in sequence or gene composition
Read the Docs: