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

Fluidigm2PURC Citation:

Blischak, P. D., M. Latvis, D. F. Morales-Briones, J. C. Johnson, V. S. Di Stilio, A. D. Wolfe, and D. C. Tank. 2018. Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons. Applications in Plant Sciences 6:e1156. [link]

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Quick Introduction

Fluidigm2PURC has two main scripts for processing paired-end amplicon sequencing data from the Fluidigm Access Array: fluidigm2purc and crunch_clusters.

• fluidigm2purc: filter and trim reads with Sickle, merge reads with FLASH2, and then process the resulting FASTQ files into FASTA files with sequence headers compatible with PURC ("PURCifying").

• crunch_clusters: infer haplotypes from PURC clustering output for diploids, polyploids, unknown ploidy, or any mix of the three.

To obtain and install Fluidigm2PURC and its required dependencies (Sickle [requires zlib], FLASH2), run the following commands in a terminal:

git clone https://github.com/pblischak/fluidigm2purc.git
cd fluidigm2purc
make
sudo make install

The crunch_clusters script can also realign and clean sequence clusters using Mafft and Phyutility, respectively. To take advantage of this functionality, install them and make sure that they are in your PATH. For Phyutility, we use the Bash script (named phyutility) setup that wraps a call to the Java phyutility.jar file.