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

PREMISE OF THE STUDY: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae). METHODS AND RESULTS: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly…

• NS
  National Science Foundation

  Awards: DEB‐1239980, DEB‐1239992, DEB‐1146295, DEB‐1240045, DEB‐0919119
• NU
  Northwestern University