HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment
By Matthew G. Johnson, E. Gardner, Yang Liu, R. Medina, B. Goffinet, A. J. Shaw, N. Zerega, N. Wickett. Applications in Plant Sciences, 2016
679 citations recorded by the source corpus.
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.
Subfields: Molecular Biology, Pharmacology, Plant Science
View Paper: https://www.semanticscholar.org/paper/c2e492473b667bbd0724b9d00f2d28e237a9554a
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Citations in the corpus
- Identifying conserved genomic elements and designing universal bait sets to enrich them (2017, methodology): “The workflow presented here differs from related efforts by combining target locus identification with enrichment bait design (Mayer et al. 2016) and because the process of conserved locus identification that I used is agnostic to the class of loci being interrogated (Johnson et al. 2016).”