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

Paul D Blischak¹, Maribeth Latvis², Diego F Morales-Briones³

¹Department of Evolution, Ecology, and Organismal Biology The Ohio State University 318 W. 12th Avenue Columbus Ohio 43210-1242 USA.

Applications in Plant Sciences

|August 23, 2018

Summary

This study introduces Fluidigm2PURC, a Python tool that automates DNA data processing for phylogenomic studies. It works with paired-end Illumina data to infer haplotypes for various ploidy levels, enhancing phylogenetic research efficiency.

Keywords:

bioinformatics haplotype inference high‐throughput sequencing microfluidic PCR phylogenomics polyploidy

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Competitive Genomic Screens of Barcoded Yeast Libraries

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Published on: August 11, 2011

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

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Published on: August 29, 2014

Amplicon Sequencing using the Long-Read Sequencing Technologies

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Published on: August 29, 2025

Area of Science:

Genomics
Bioinformatics
Evolutionary Biology

Background:

Targeted enrichment strategies efficiently collect DNA sequence data for phylogenomic inference.
Automated and reproducible data processing is essential for phylogenetic studies.

Purpose of the Study:

To present Fluidigm2PURC, an open-source Python utility for processing paired-end Illumina data.
To enable automated and reproducible analysis of phylogenomic data.

Main Methods:

Developed Fluidigm2PURC, a Python utility for processing double-barcoded PCR amplicon data.
Integrated Fluidigm2PURC with the PURC (Pipeline for Untangling Reticulate Complexes) program.
Processed raw FASTQ files for PURC analysis and inferred haplotypes for various ploidy levels.

Main Results:

Fluidigm2PURC successfully processes paired-end Illumina data.
The pipeline infers haplotypes for diploids, polyploids, and samples with unknown ploidy.
Demonstrated utility with a dataset from the genus Thalictrum (Ranunculaceae).

Conclusions:

Fluidigm2PURC is freely available on GitHub for Unix-like systems.
The utility is also accessible via Docker for all operating systems.
Fluidigm2PURC facilitates efficient and reproducible phylogenomic data analysis.