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Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons

TitleFluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons
Publication TypeJournal Article
Year of Publication2018
AuthorsBlischak PD, Latvis M, Morales-Briones DF, Johnson JC, Di Stilio VS, Wolfe AD, Tank DC
JournalApplications in Plant Sciences
Volume6
Start Pagee01156
Issue6
Date Published06/2018
Abstract

Premise of the study: Targeted enrichment strategies for phylogenomic inference are a time- and cost-efficient way to collect DNA sequence data for large numbers of individuals at multiple, independent loci. Automated and reproducible processing of these data is a crucial step for researchers conducting phylogenetic studies. Methods and Results: We present Fluidigm2PURC, an open source Python utility for processing paired-end Illumina data from double-barcoded PCR amplicons. In combination with the program PURC (Pipeline for Untangling Reticulate Complexes), our scripts process raw FASTQ files for analysis with PURC and use its output to infer haplotypes for diploids, polyploids, and samples with unknown ploidy. We demonstrate the use of the pipeline with an example data set from the genus Thalictrum L. (Ranunculaceae). Conclusions: Fluidigm2PURC is freely available for Unix-like operating systems on GitHub [https://github.com/pblischak/fluidigm2purc] and for all operating systems through Docker [https://hub.docker.com/r/pblischak/fluidigm2purc].

URLhttps://onlinelibrary.wiley.com/doi/abs/10.1002/aps3.1156
DOI10.1002/aps3.1156
Fields of interest: