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

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 f

SUBMITTER: Blischak PD 

PROVIDER: S-EPMC6025812 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature