Please note that Kairos is currently under active development.
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
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