Open AccessHybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment
Author(s) -
Johnson Matthew G.,
Gardner Elliot M.,
Liu Yang,
Medina Rafael,
Goffinet Bernard,
Shaw A. Jonathan,
Zerega Nyree J. C.,
Wickett Norman J.
Publication year - 2016
Publication title -
applications in plant sciences
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.64
H-Index - 23
ISSN - 2168-0450
DOI - 10.3732/apps.1600016
Subject(s) - biology , contig , intron , gene , sequence (biology) , phylogenetic tree , computational biology , sequence assembly , genetics , phylogenetics , genome , transcriptome , gene expression
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).