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Bioinformatics. 2010 Jul 15;26(14):1783-5. doi: 10.1093/bioinformatics/btq281. Epub 2010 Jun 18.

Manipulation of FASTQ data with Galaxy.

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1
Huck Institute for the Life Sciences, Penn State University, University Park, PA 16803, USA.

Abstract

SUMMARY:

Here, we describe a tool suite that functions on all of the commonly known FASTQ format variants and provides a pipeline for manipulating next generation sequencing data taken from a sequencing machine all the way through the quality filtering steps.

AVAILABILITY AND IMPLEMENTATION:

This open-source toolset was implemented in Python and has been integrated into the online data analysis platform Galaxy (public web access: http://usegalaxy.org; download: http://getgalaxy.org). Two short movies that highlight the functionality of tools described in this manuscript as well as results from testing components of this tool suite against a set of previously published files are available at http://usegalaxy.org/u/dan/p/fastq

PMID:
20562416
PMCID:
PMC2894519
DOI:
10.1093/bioinformatics/btq281
[Indexed for MEDLINE]
Free PMC Article
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