title: HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment.
abstract: OBJECTIVE
  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).
  
  
  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 complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus.
  
  
  CONCLUSIONS
  HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper.
authors.affiliation: Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, Illinois 60022 USA.
authors.forename: Matthew G
authors.initials: MG
authors.lastname: Johnson
authors.affiliation: Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, Illinois 60022 USA; Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208 USA.
authors.forename: Elliot M
authors.initials: EM
authors.lastname: Gardner
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Storrs, Connecticut 06269 USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Storrs, Connecticut 06269 USA.
authors.forename: Rafael
authors.initials: R
authors.lastname: Medina
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Storrs, Connecticut 06269 USA.
authors.forename: Bernard
authors.initials: B
authors.lastname: Goffinet
authors.affiliation: Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708 USA.
authors.forename: A Jonathan
authors.initials: AJ
authors.lastname: Shaw
authors.affiliation: Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, Illinois 60022 USA; Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208 USA.
authors.forename: Nyree J C
authors.initials: NJ
authors.lastname: Zerega
authors.affiliation: Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, Illinois 60022 USA; Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208 USA.
authors.forename: Norman J
authors.initials: NJ
authors.lastname: Wickett
keywords: Hyb-Seq; bioinformatics; phylogenomics; sequence assembly