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

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.