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Manipulation of FASTQ data with Galaxy
Open accessAbstract
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 Contact: james.taylor@emory.edu; anton@bx.psu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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Research works printed but not linked: 4
- Blankenberg, 2007, A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly, Genome Res., 17, 960, 10.1101/gr.5578007 · DOI
- Blankenberg, 2010, Galaxy: a web-based genome analysis tool for experimentalists, Curr. Protoc. Mol. Biol., 10.1002/0471142727.mb1910s89 · DOI · Paper page
- Cock, 2009, The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants, Nucleic Acids Res., 38, 1767, 10.1093/nar/gkp1137 · DOI · Paper page
- Taylor, 2007, Using galaxy to perform large-scale interactive data analyses, Curr. Protoc. Bioinformatics, 10.1002/0471250953.bi1005s19 · DOI
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Metadata
- Authors
- Blankenberg, D., Gordon, A., Von Kuster, G., Coraor, N., Taylor, J., Nekrutenko, A., & the Galaxy Team
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-06-18
- Volume
- 26
- Issue
- 14
- Pages
- 1783-1785
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2107493728
- Cited by
- 683
- References
- 0
- FWCI
- 8.86
- Type
- journal article
- Language
- en
- Open access
- hybrid
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