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Johnson MG, Gardner EM, Liu Y, et al. HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Appl Plant Sci. 2016;4(7)doi: 10.3732/apps.1600016.
Johnson, M. G., Gardner, E. M., Liu, Y., Medina, R., Goffinet, B., Shaw, A. J., Zerega, N. J., & Wickett, N. J. (2016). HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Applications in plant sciences, 4(7), . https://doi.org/10.3732/apps.1600016
Johnson, Matthew G, et al. "HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment." Applications in plant sciences vol. 4,7 (2016). doi: https://doi.org/10.3732/apps.1600016
Johnson MG, Gardner EM, Liu Y, Medina R, Goffinet B, Shaw AJ, Zerega NJ, Wickett NJ. HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Appl Plant Sci. 2016 Jul 12;4(7). doi: 10.3732/apps.1600016. eCollection 2016 Jul. PMID: 27437175; PMCID: PMC4948903.
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Appl Plant Sci. 2016 Jul 12;4(7). doi: 10.3732/apps.1600016. eCollection 2016 Jul.

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

Applications in plant sciences

Matthew G Johnson, Elliot M Gardner, Yang Liu, Rafael Medina, Bernard Goffinet, A Jonathan Shaw, Nyree J C Zerega, Norman J Wickett

Affiliations

  1. Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, Illinois 60022 USA.
  2. Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, Illinois 60022 USA; Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208 USA.
  3. Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Storrs, Connecticut 06269 USA.
  4. Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708 USA.

PMID: 27437175 PMCID: PMC4948903 DOI: 10.3732/apps.1600016

Abstract

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 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.

Keywords: Hyb-Seq; bioinformatics; phylogenomics; sequence assembly

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