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• W2950275816 abstract "Abstract Horizontal gene transfer (HGT) is a fundamental mechanism that enables organisms such as bacteria to directly transfer genetic material between distant species. This way, bacteria can acquire new traits such as antibiotic resistance or pathogenic toxins. Current bioinfor-matics approaches focus on the detection of past HGT events by exploring phylogenetic trees or genome composition inconsistencies. However, this normally requires the availability of finished and fully annotated genomes and of sufficiently large deviations that allow detection. Thus, these techniques are not widely applicable. Especially in an outbreak scenario where new HGT mediated pathogens emerge, there is need for fast and precise HGT detection. Next-generation sequencing (NGS) technologies can facilitate swift analysis of unknown pathogens but, to the best of our knowledge, so far no approach uses NGS data directly to detect HGTs. We present Daisy, a novel mapping-based tool for HGT detection directly from NGS data. Daisy determines HGT boundaries with split-read mapping and evaluates candidate regions relying on read pair and coverage information. Daisy can successfully detect 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. Daisy is freely available from http://github.com/ktrappe/daisy ." @default.
• W2950275816 created "2019-06-27" @default.
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• W2950275816 date "2016-02-11" @default.
• W2950275816 modified "2023-10-16" @default.
• W2950275816 title "Detecting Horizontal Gene Transfer by Mapping Sequencing Reads Across Species Boundaries" @default.
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• W2950275816 doi "https://doi.org/10.1101/039495" @default.
• W2950275816 hasPublicationYear "2016" @default.
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