Detecting horizontal gene transfer by mapping sequencing reads across species boundaries

We present Daisy, a novel mapping-based tool for HGT detection. Daisy determines HGT boundaries with split-read mapping and evaluates candidate regions relying on read pair and coverage information. Daisy successfully detects HGT regions with base pair resolution in both simulated and real data, and outperforms alternative approaches using a genome assembly of the reads. We see our approach as a powerful complement for a comprehensive analysis of HGT in the context of NGS data. Availability and Implementation: Daisy is freely available from http://github.com/ktrappe/daisy. Contact: renardb@rki.de Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - Category: Bioinformatics Authors: Tags: GENES Source Type: research