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

Paul D. Blischak, Maribeth Latvis, Diego F. Morales-Briones, Jens C. Johnson, Verónica S. Di Stilio, Andrea D. Wolfe, David C. Tank

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

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 (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).

Original languageEnglish (US)
Article numbere01156
JournalApplications in Plant Sciences
Volume6
Issue number6
DOIs
StatePublished - Jun 2018

Bibliographical note

Funding Information:
The authors thank C. Rothfels for helpful discussions regarding the use of PURC. We also thank S. Uribe-Convers for providing valuable feedback while testing the Fluidigm2PURC code. This work was supported by the following grants from the National Science

Publisher Copyright:
Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America

Keywords

  • bioinformatics
  • haplotype inference
  • high-throughput sequencing
  • microfluidic PCR
  • phylogenomics
  • polyploidy

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