MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches

Metagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets or require reference genomes. Here, we present MetaCHIP, a pipeline for reference-independent HGT identification at the community level.Assessment of MetaCHIP's performance on simulated datasets revealed that it can predict HGTs with various...