Manipulation of FASTQ data with Galaxy.
CONCLUSIONS
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.


METHODS
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
Blankenberg
Daniel
D
Huck Institute for the Life Sciences, Penn State University, University Park, PA 16803, USA.
Gordon
Assaf
A
Von Kuster
Gregory
G
Coraor
Nathan
N
Taylor
James
J
Nekrutenko
Anton
A
D016208:Databases, Factual; D023281:Genomics / Q000379:methods*; D020407:Internet; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D014584:User-Computer Interface