HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

• Published in: Applications in plant sciences Vol. 4; no. 7
• Main Authors: Johnson, Matthew G, Gardner, Elliot M, Liu, Yang, Medina, Rafael, Goffinet, Bernard, Shaw, A. Jonathan, Zerega, Nyree J. C, Wickett, Norman J
• Format: Journal Article
• Language: English
• Published: United States Botanical Society of America 01.07.2016; John Wiley & Sons, Inc
• Subjects: Artocarpus; baits; Bioinformatics; computer software; Deoxyribonucleic acid; DNA; exons; Gene mapping; Genes; Genomes; high-throughput nucleotide sequencing; Hyb-Seq; Introns; loci; Phylogenetics; phylogenomics; Phylogeny; Plant sciences; Scripts; sequence assembly; Software Note; SOFTWARE NOTES; United States > US; sequence assembly; Hyb-Seq; phylogenomics; bioinformatics

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...