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

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. HybPi

SUBMITTER: Johnson MG 

PROVIDER: S-EPMC4948903 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature