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

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).