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

Manipulation of FASTQ data with Galaxy

Daniel Blankenberg  1 , Assaf Gordon, Gregory Von Kuster, Nathan Coraor, James Taylor, Anton Nekrutenko; Galaxy Team
Affiliations

Manipulation of FASTQ data with Galaxy

Daniel Blankenberg et al. Bioinformatics. .

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

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References

    1. Blankenberg D, et al. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007;17:960–964. - PMC - PubMed
    1. Blankenberg D, et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol. 2010 Chapter 19, Unit 19.10.1-21. - PMC - PubMed
    1. Cock PJ, et al. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009;38:1767–1771. - PMC - PubMed
    1. Taylor J, et al. Using galaxy to perform large-scale interactive data analyses. Curr. Protoc. Bioinformatics. 2007 Chapter 10, Unit 10.5. - PMC - PubMed

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