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      Manipulation of FASTQ data with Galaxy

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          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

          Contact: james.taylor@ 123456emory.edu ; anton@ 123456bx.psu.edu

          Supplementary information: Supplementary data are available at Bioinformatics online.

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          Galaxy: a web-based genome analysis tool for experimentalists.

          Daniel Blankenberg, Gregory Von Kuster, Nathaniel Coraor … (2010)
          High-throughput data production has revolutionized molecular biology. However, massive increases in data generation capacity require analysis approaches that are more sophisticated, and often very computationally intensive. Thus, making sense of high-throughput data requires informatics support. Galaxy (http://galaxyproject.org) is a software system that provides this support through a framework that gives experimentalists simple interfaces to powerful tools, while automatically managing the computational details. Galaxy is distributed both as a publicly available Web service, which provides tools for the analysis of genomic, comparative genomic, and functional genomic data, or a downloadable package that can be deployed in individual laboratories. Either way, it allows experimentalists without informatics or programming expertise to perform complex large-scale analysis with just a Web browser.
          Article 0 comments Cited 202 times – based on 0 reviews     Review now
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            A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.

            Yi Zhang, Istvan Albert, Johnny He … (2007)
            The standardization and sharing of data and tools are the biggest challenges of large collaborative projects such as the Encyclopedia of DNA Elements (ENCODE). Here we describe a compact Web application, Galaxy2(ENCODE), that effectively addresses these issues. It provides an intuitive interface for the deposition and access of data, and features a vast number of analysis tools including operations on genomic intervals, utilities for manipulation of multiple sequence alignments, and molecular evolution algorithms. By providing a direct link between data and analysis tools, Galaxy2(ENCODE) allows addressing biological questions that are beyond the reach of existing software. We use Galaxy2(ENCODE) to show that the ENCODE regions contain >2000 unannotated transcripts under strong purifying selection that are likely functional. We also show that the ENCODE regions are representative of the entire genome by estimating the rate of nucleotide substitution and comparing it to published data. Although each of these analyses is complex, none takes more than 15 min from beginning to end. Finally, we demonstrate how new tools can be added to Galaxy2(ENCODE) with almost no effort. Every section of the manuscript is supplemented with QuickTime screencasts. Galaxy2(ENCODE) and the screencasts can be accessed at http://g2.bx.psu.edu.
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              Using galaxy to perform large-scale interactive data analyses.

              Paul William James Taylor, Anton Nekrutenko, Dan Blankenberg … (2007)
              While most experimental biologists know where to download genomic data, few have a concrete plan on how to analyze it. This situation can be corrected by: (1) providing unified portals serving genomic data and (2) building Web applications to allow flexible retrieval and on-the-fly analyses of the data. Powerful resources, such as the UCSC Genome Browser already address the first issue. The second issue, however, remains open. For example, how to find human protein-coding exons with the highest density of single nucleotide polymorphisms (SNPs) and extract orthologous sequences from all sequenced mammals? Indeed, one can access all relevant data from the UCSC Genome Browser. But once the data is downloaded how would one deal with millions of SNPs and gigabytes of alignments? Galaxy (http://g2.bx.psu.edu) is designed specifically for that purpose. It amplifies the strengths of existing resources (such as UCSC Genome Browser) by allowing the user to access and, most importantly, analyze data within a single interface in an unprecedented number of ways. Copyright 2007 by John Wiley & Sons, Inc.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Bioinformatics
                Journal ID (publisher-id): bioinformatics
                Journal ID (hwp): bioinfo
                Title: Bioinformatics
                Publisher: Oxford University Press
                ISSN (Print): 1367-4803
                ISSN (Electronic): 1367-4811
                Publication date (Print): 15 July 2010
                Publication date (Electronic): 18 June 2010
                Publication date PMC-release: 18 June 2010
                Volume: 26
                Issue: 14
                Pages: 1783-1785
                Affiliations
                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
                Author notes
                * To whom correspondence should be addressed.

                † The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

                ‡ http://galaxyproject.org

                Associate Editor: John Quackenbush

                Article
                Publisher ID: btq281
                DOI: 10.1093/bioinformatics/btq281
                PMC ID: 2894519
                PubMed ID: 20562416
                SO-VID: 49e218cf-67c8-4b68-bc12-3d2dbedf3914
                Copyright © © The Author(s) 2010. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 1 April 2010
                Date revision received : 20 May 2010
                Date accepted : 24 May 2010
                Categories
                Subject: Applications Note
                Subject: Sequence Analysis

                ScienceOpen disciplines: Bioinformatics & Computational biology
                Data availability:
                ScienceOpen disciplines: Bioinformatics & Computational biology

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