HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target...

Area of Science:

• Bioinformatics
• Phylogenetics
• Genomics

Background:

• Target enrichment sequencing generates high-throughput reads requiring reassembly into loci for phylogenetic analysis.
• Bioinformatics challenges exist in assembling these reads into accurate gene regions.
• Efficient assembly is crucial for robust phylogenetic studies.

Purpose of the Study:

• To develop a user-friendly platform, HybPiper, for assembling gene regions from target enrichment data.
• To enable extraction of exon and intron sequences.
• To facilitate the identification of paralogous gene copies.

Main Methods:

• HybPiper employs a three-phase parallel execution pipeline: read mapping, contig assembly, and target sequence extraction.
• The platform was tested using baits for 333 phylogenetic markers and 125 functional genes in Artocarpus.
• Tested on 22 species within the Artocarpus genus.

Main Results:

• HybPiper successfully recovered nearly complete gene sequences for all targeted genes across 22 Artocarpus species.
• The pipeline recovered over 500 bp of non-targeted intron sequence for more than half of the phylogenetic markers.
• Paralogous gene copies were effectively identified within the Artocarpus dataset.

Conclusions:

• HybPiper provides a robust solution for assembling gene regions and extracting sequence data for phylogenetic studies.
• The platform is designed for Linux and Mac OS X operating systems.
• HybPiper is freely available for download, promoting wider adoption in the research community.