{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T06:32:30Z","timestamp":1780554750939,"version":"3.54.1"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"vor","delay-in-days":2297,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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<\/jats:p>\n               <jats:p>Contact: \u00a0james.taylor@emory.edu; anton@bx.psu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq281","type":"journal-article","created":{"date-parts":[[2010,6,20]],"date-time":"2010-06-20T19:54:25Z","timestamp":1277063665000},"page":"1783-1785","source":"Crossref","is-referenced-by-count":587,"title":["Manipulation of FASTQ data with Galaxy"],"prefix":"10.1093","volume":"26","author":[{"given":"Daniel","family":"Blankenberg","sequence":"first","affiliation":[{"name":"1 Huck Institute for the Life Sciences, Penn State University, University Park, PA 16803, 2 Cold Spring Harbor Laboratory, Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724 and 3 Departments of Biology and Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Assaf","family":"Gordon","sequence":"additional","affiliation":[{"name":"1 Huck Institute for the Life Sciences, Penn State University, University Park, PA 16803, 2 Cold Spring Harbor Laboratory, Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724 and 3 Departments of Biology and Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory","family":"Von Kuster","sequence":"additional","affiliation":[{"name":"1 Huck Institute for the Life Sciences, Penn State University, University Park, PA 16803, 2 Cold Spring Harbor Laboratory, Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724 and 3 Departments of Biology and Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathan","family":"Coraor","sequence":"additional","affiliation":[{"name":"1 Huck Institute for the Life Sciences, Penn State University, University Park, PA 16803, 2 Cold Spring Harbor Laboratory, Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724 and 3 Departments of Biology and Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Taylor","sequence":"additional","affiliation":[{"name":"1 Huck Institute for the Life Sciences, Penn State University, University Park, PA 16803, 2 Cold Spring Harbor Laboratory, Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724 and 3 Departments of Biology and Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anton","family":"Nekrutenko","sequence":"additional","affiliation":[{"name":"1 Huck Institute for the Life Sciences, Penn State University, University Park, PA 16803, 2 Cold Spring Harbor Laboratory, Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724 and 3 Departments of Biology and Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"name":"the Galaxy Team","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2010,6,18]]},"reference":[{"key":"2023012507592212800_B1","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1101\/gr.5578007","article-title":"A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly","volume":"17","author":"Blankenberg","year":"2007","journal-title":"Genome Res."},{"key":"2023012507592212800_B2","doi-asserted-by":"crossref","DOI":"10.1002\/0471142727.mb1910s89","article-title":"Galaxy: a web-based genome analysis tool for experimentalists","author":"Blankenberg","year":"2010","journal-title":"Curr. Protoc. Mol. Biol."},{"key":"2023012507592212800_B3","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1093\/nar\/gkp1137","article-title":"The Sanger FASTQ file format for sequences with quality scores, and the Solexa\/Illumina FASTQ variants","volume":"38","author":"Cock","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012507592212800_B4","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi1005s19","article-title":"Using galaxy to perform large-scale interactive data analyses","author":"Taylor","year":"2007","journal-title":"Curr. Protoc. 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