Bioinformatics. 2010 Jul 15;26(14):1783-5. Epub 2010 Jun 18.

Manipulation of FASTQ data with Galaxy.

Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team.

Source

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; [PubMed - indexed for MEDLINE]
PMCID:: PMC2894519

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