https://github.com/pblischak/fluidigm2purc

Automated processing and haplotype inference for double-barcoded PCR amplicons
https://github.com/pblischak/fluidigm2purc

fluidigm high-throughput-sequencing phylogenomics polyploid

Last synced: 5 months ago
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Automated processing and haplotype inference for double-barcoded PCR amplicons

• Host: GitHub
• URL: https://github.com/pblischak/fluidigm2purc
• Owner: pblischak
• License: gpl-3.0
• Created: 2017-04-11T21:40:37.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2019-02-05T20:48:01.000Z (over 6 years ago)
• Last Synced: 2025-02-17T07:44:48.460Z (8 months ago)
• Topics: fluidigm, high-throughput-sequencing, phylogenomics, polyploid
• Language: Python
• Homepage: https://fluidigm2purc.readthedocs.io
• Size: 474 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

          
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## **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]](https://doi.org/10.1002/aps3.1156)

## [**Read the Docs**](http://fluidigm2purc.readthedocs.io/en/latest/?badge=latest)

### 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](https://github.com/najoshi/sickle) [requires zlib],

[FLASH2](https://github.com/dstreett/FLASH2)),

run the following commands in a terminal:

```bash

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](http://mafft.cbrc.jp/alignment/software/) and

[Phyutility](https://github.com/blackrim/phyutility/releases/tag/v2.7.1), 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.