Objective review of de novo stand‐alone error correction methods for NGS data
Identifieur interne : 000102 ( Istex/Corpus ); précédent : 000101; suivant : 000103Objective review of de novo stand‐alone error correction methods for NGS data
Auteurs : Andy S. Alic ; David Ruzafa ; Joaquin Dopazo ; Ignacio BlanquerSource :
- Wiley Interdisciplinary Reviews: Computational Molecular Science [ 1759-0876 ] ; 2016-03.
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DOI: 10.1002/wcms.1239
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ISTEX:DB06F37CA718C5C4951BE55F6D594A1DB45132F3Le document en format XML
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S.</forename><surname>Alic</surname></persName><affiliation><orgName type="division">Institute of Instrumentation for Molecular Imaging (I3M)</orgName><orgName type="institution">Universitat Politècnica de València</orgName><address><settlement>València</settlement><country key="ES" xml:lang="en">SPAIN</country></address></affiliation></author><author xml:id="author-0001"><persName><forename type="first">David</forename><surname>Ruzafa</surname></persName><affiliation><orgName type="division">Departamento de Quìmica Fìsica e Instituto de Biotecnologìa, Facultad de Ciencias</orgName><orgName type="institution">Universidad de Granada</orgName><address><settlement>Granada</settlement><country key="ES" xml:lang="en">SPAIN</country></address></affiliation></author><author xml:id="author-0002"><persName><forename type="first">Joaquin</forename><surname>Dopazo</surname></persName><affiliation><orgName type="division">Department of Computational Genomics</orgName><orgName type="institution">Príncipe Felipe Research Centre (CIPF)</orgName><address><settlement>Valencia</settlement><country key="ES" xml:lang="en">SPAIN</country></address></affiliation><affiliation><orgName type="institution">CIBER de Enfermedades Raras (CIBERER)</orgName><address><settlement>Valencia</settlement><country key="ES" xml:lang="en">SPAIN</country></address></affiliation><affiliation><orgName type="institution">Functional Genomics Node (INB) at CIPF</orgName><address><settlement>Valencia</settlement><country key="ES" xml:lang="en">SPAIN</country></address></affiliation></author><author xml:id="author-0003"><persName><forename type="first">Ignacio</forename><surname>Blanquer</surname></persName><affiliation><orgName type="division">Institute of Instrumentation for Molecular Imaging (I3M)</orgName><orgName type="institution">Universitat Politècnica de València</orgName><address><settlement>València</settlement><country key="ES" xml:lang="en">SPAIN</country></address></affiliation><affiliation><orgName type="division">Biomedical Imaging Research Group GIBI 2<hi rend="superscript">30</hi></orgName><orgName type="institution">Polytechnic University Hospital La Fe</orgName><address><settlement>Valencia</settlement><country key="ES" xml:lang="en">SPAIN</country></address></affiliation></author><idno type="istex">DB06F37CA718C5C4951BE55F6D594A1DB45132F3</idno><idno type="ark">ark:/67375/WNG-VGWGTPZK-P</idno><idno type="DOI">10.1002/wcms.1239</idno><idno type="unit">WCMS1239</idno><idno type="toTypesetVersion">file:WCMS.WCMS1239.pdf</idno></analytic><monogr><title level="j" type="main">Wiley Interdisciplinary Reviews: Computational Molecular Science</title><title level="j" type="alt">WILEY INTERDISCIPLINARY REVIEWS: COMPUTATIONAL MOLECULAR SCIENCE</title><idno type="pISSN">1759-0876</idno><idno type="eISSN">1759-0884</idno><idno type="book-DOI">10.1111/(ISSN)1759-0884</idno><idno type="book-part-DOI">10.1002/wcms.2016.6.issue-2</idno><idno type="product">WCMS</idno><imprint><biblScope unit="vol">6</biblScope><biblScope unit="issue">2</biblScope><biblScope unit="page" from="111">111</biblScope><biblScope unit="page" to="146">146</biblScope><biblScope unit="page-count">1</biblScope><publisher>Wiley Periodicals, Inc.</publisher><pubPlace>Hoboken, USA</pubPlace><date type="published" when="2016-03"></date></imprint></monogr></biblStruct></sourceDesc></fileDesc><encodingDesc><schemaRef type="ODD" url="https://xml-schema.delivery.istex.fr/tei-istex.odd"></schemaRef><appInfo><application ident="pub2tei" version="1.0.10" when="2019-12-20"><label>pub2TEI-ISTEX</label><desc>A set of style sheets for converting XML documents encoded in various scientific publisher formats into a common TEI format.
<ref target="http://www.tei-c.org/">We use TEI</ref></desc></application></appInfo></encodingDesc><profileDesc><abstract style="graphical" xml:id="wcms1239-abs-0001"><p xml:id="wcms1239-para-0601"><figure type="box"><media mimeType="image" url="urn:x-wiley:17590876:media:wcms1239:wcms1239-toc-0001"></media></figure></p></abstract><abstract style="main" xml:id="wcms1239-abs-0002"><p xml:id="wcms1239-para-0001">The sequencing market has increased steadily over the last few years, with different approaches to read <hi rend="fc">DNA</hi> information prone to different types of errors. Multiple studies demonstrated the impact of sequencing errors on different applications of next‐generation sequencing (<hi rend="fc">NGS</hi>), making error correction a fundamental initial step. Different methods in the literature use different approaches and fit different types of problems. We analyzed 50 methods divided into five main approaches (k‐spectrum, suffix arrays, multiple‐sequence alignment, read clustering, and probabilistic models). They are not published as a part of a suite (stand‐alone), and target raw, unprocessed data without an existing reference genome (<hi rend="fi">de novo</hi>). These correctors handle one or more sequencing technologies using the same or different approaches. They face general challenges (sometimes with specific traits for specific technologies) such as repetitive regions, uncalled bases, and ploidy. Even assessing their performance is a challenge in itself because of the approach taken by various authors, the unknown factor (<hi rend="fi">de novo</hi>), and the behavior of the third‐party tools employed in the benchmarks. This study aims to help the researcher in the field to advance the field of error correction, the educator to have a brief but comprehensive companion, and the bioinformatician to choose the right tool for the right job. <hi rend="italic">WIREs Comput Mol Sci</hi> 2016, 6:111–146. doi: 10.1002/wcms.1239</p><p>For further resources related to this article, please visit the <ref type="url">http://wires.wiley.com/remdoi.cgi?doi=10.1002/wcms.1194</ref>.</p></abstract><textClass><keywords rend="articleCategory"><term>Advanced Review</term></keywords><keywords rend="tocHeading1"><term>Advanced Reviews</term></keywords></textClass><textClass><keywords ana="subject"><term ref="http://psi.wiley.com/subject/17590876/CBAD">Computer Algorithms and Programming</term></keywords></textClass><langUsage><language ident="en"></language></langUsage></profileDesc><revisionDesc><change when="2019-12-20" who="#istex" 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Interdisciplinary Reviews: Computational Molecular Science</title><title type="short">WIREs Comput Mol Sci</title></titleGroup></publicationMeta><publicationMeta level="part" position="20"><doi origin="wiley">10.1002/wcms.2016.6.issue-2</doi><copyright ownership="publisher">© 2016 John Wiley & Sons, Ltd.</copyright><numberingGroup><numbering type="journalVolume" number="6">6</numbering><numbering type="journalIssue">2</numbering></numberingGroup><coverDate startDate="2016-03">March/April 2016</coverDate></publicationMeta><publicationMeta level="unit" position="50" type="reviewArticle" status="forIssue"><doi>10.1002/wcms.1239</doi><idGroup><id type="unit" value="WCMS1239"></id></idGroup><countGroup><count type="pageTotal" number="1"></count></countGroup><titleGroup><title type="articleCategory">Advanced Review</title><title type="tocHeading1">Advanced Reviews</title></titleGroup><copyright ownership="publisher">© 2016 John Wiley & Sons, Ltd.</copyright><eventGroup><event type="manuscriptReceived" date="2015-07-02"></event><event type="manuscriptRevised" date="2015-11-06"></event><event type="manuscriptAccepted" date="2015-11-06"></event><event type="xmlCreated" agent="Laserwords Private Ltd." date="2015-11-30"></event><event type="publishedOnlineEarlyUnpaginated" date="2016-01-11"></event><event type="publishedOnlineFinalForm" date="2016-02-25"></event><event type="firstOnline" date="2016-01-11"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:5.0.6 mode:FullText" date="2017-02-10"></event></eventGroup><numberingGroup><numbering type="pageFirst">111</numbering><numbering type="pageLast">146</numbering></numberingGroup><correspondenceTo>Correspondence to: <email>asalic@posgrado.upv.es</email></correspondenceTo><subjectInfo><subject href="http://psi.wiley.com/subject/17590876/CBAD">Computer Algorithms and Programming</subject></subjectInfo><linkGroup><link type="toTypesetVersion" href="file:WCMS.WCMS1239.pdf"></link></linkGroup></publicationMeta><contentMeta><titleGroup><title type="main">Objective review of <fi>de novo</fi> stand‐alone error correction methods for <fc>NGS</fc> data</title><title type="short">Objective review of de novo stand‐alone NGS correctors</title></titleGroup><creators><creator creatorRole="author" xml:id="wcms1239-cr-0001" affiliationRef="#wcms1239-aff-0001" corresponding="yes"><personName><givenNames>Andy S.</givenNames><familyName>Alic</familyName></personName></creator><creator creatorRole="author" xml:id="wcms1239-cr-0002" affiliationRef="#wcms1239-aff-0002"><personName><givenNames>David</givenNames><familyName>Ruzafa</familyName></personName></creator><creator creatorRole="author" xml:id="wcms1239-cr-0003" affiliationRef="#wcms1239-aff-0003 #wcms1239-aff-0004 #wcms1239-aff-0005"><personName><givenNames>Joaquin</givenNames><familyName>Dopazo</familyName></personName></creator><creator creatorRole="author" xml:id="wcms1239-cr-0004" affiliationRef="#wcms1239-aff-0001 #wcms1239-aff-0006"><personName><givenNames>Ignacio</givenNames><familyName>Blanquer</familyName></personName></creator></creators><affiliationGroup xml:id="wcms1239-affgp-0001"><affiliation countryCode="ES" type="organization" xml:id="wcms1239-aff-0001"><orgDiv>Institute of Instrumentation for Molecular Imaging (I3M)</orgDiv><orgName>Universitat Politècnica de València</orgName><address><city>València</city><country>Spain</country></address></affiliation><affiliation countryCode="ES" type="organization" xml:id="wcms1239-aff-0002"><orgDiv>Departamento de Quìmica Fìsica e Instituto de Biotecnologìa, Facultad de Ciencias</orgDiv><orgName>Universidad de Granada</orgName><address><city>Granada</city><country>Spain</country></address></affiliation><affiliation countryCode="ES" type="organization" xml:id="wcms1239-aff-0003"><orgDiv>Department of Computational Genomics</orgDiv><orgName>Príncipe Felipe Research Centre (CIPF)</orgName><address><city>Valencia</city><country>Spain</country></address></affiliation><affiliation countryCode="ES" type="organization" xml:id="wcms1239-aff-0004"><orgName>CIBER de Enfermedades Raras (CIBERER)</orgName><address><city>Valencia</city><country>Spain</country></address></affiliation><affiliation countryCode="ES" type="organization" xml:id="wcms1239-aff-0005"><orgName>Functional Genomics Node (INB) at CIPF</orgName><address><city>Valencia</city><country>Spain</country></address></affiliation><affiliation countryCode="ES" type="organization" xml:id="wcms1239-aff-0006"><orgDiv>Biomedical Imaging Research Group GIBI 2<sup>30</sup></orgDiv><orgName>Polytechnic University Hospital La Fe</orgName><address><city>Valencia</city><country>Spain</country></address></affiliation></affiliationGroup><fundingInfo><fundingAgency fundRefName="Generalitat Valenciana" funderDoi="10.13039/501100003359">Generalitat Valenciana</fundingAgency><fundingNumber>GRISOLIA/2013/013</fundingNumber></fundingInfo><abstractGroup><abstract type="graphical" xml:id="wcms1239-abs-0001"><p xml:id="wcms1239-para-0601"><blockFixed xml:id="wcms1239-blkfxd-0001" type="graphic"><mediaResourceGroup><mediaResource href="urn:x-wiley:17590876:media:wcms1239:wcms1239-toc-0001" alt="image"></mediaResource></mediaResourceGroup></blockFixed></p></abstract><abstract type="main" xml:id="wcms1239-abs-0002"><p xml:id="wcms1239-para-0001">The sequencing market has increased steadily over the last few years, with different approaches to read <fc>DNA</fc> information prone to different types of errors. Multiple studies demonstrated the impact of sequencing errors on different applications of next‐generation sequencing (<fc>NGS</fc>), making error correction a fundamental initial step. Different methods in the literature use different approaches and fit different types of problems. We analyzed 50 methods divided into five main approaches (k‐spectrum, suffix arrays, multiple‐sequence alignment, read clustering, and probabilistic models). They are not published as a part of a suite (stand‐alone), and target raw, unprocessed data without an existing reference genome (<fi>de novo</fi>). These correctors handle one or more sequencing technologies using the same or different approaches. They face general challenges (sometimes with specific traits for specific technologies) such as repetitive regions, uncalled bases, and ploidy. Even assessing their performance is a challenge in itself because of the approach taken by various authors, the unknown factor (<fi>de novo</fi>), and the behavior of the third‐party tools employed in the benchmarks. This study aims to help the researcher in the field to advance the field of error correction, the educator to have a brief but comprehensive companion, and the bioinformatician to choose the right tool for the right job. <i>WIREs Comput Mol Sci</i> 2016, 6:111–146. doi: 10.1002/wcms.1239</p><p>For further resources related to this article, please visit the <url href="http://wires.wiley.com/remdoi.cgi?doi=10.1002/wcms.1194">WIREs website</url>.</p></abstract></abstractGroup></contentMeta><noteGroup xml:id="wcms1239-ntgp-0001"><note xml:id="wcms1239-note-0001" numbered="no">Conflict of interest: The authors have declared no conflicts of interest for this article.</note><note xml:id="wcms1239-note-0002" numbered="no">Additional Supporting Information may be found in the online version of this article.</note></noteGroup></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Objective review of de novo stand‐alone error correction methods for NGS data</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Objective review of de novo stand‐alone NGS correctors</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Objective review of de novo stand‐alone error correction methods for NGS data</title></titleInfo><name type="personal"><namePart type="given">Andy S.</namePart><namePart type="family">Alic</namePart><affiliation>Institute of Instrumentation for Molecular Imaging (I3M), Universitat Politècnica de València, València, Spain</affiliation><affiliation>E-mail: asalic@posgrado.upv.es</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">David</namePart><namePart type="family">Ruzafa</namePart><affiliation>Departamento de Quìmica Fìsica e Instituto de Biotecnologìa, Facultad de Ciencias, Universidad de Granada, Granada, Spain</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Joaquin</namePart><namePart type="family">Dopazo</namePart><affiliation>Department of Computational Genomics, Príncipe Felipe Research Centre (CIPF), Valencia, Spain</affiliation><affiliation>CIBER de Enfermedades Raras (CIBERER), Valencia, Spain</affiliation><affiliation>Functional Genomics Node (INB) at CIPF, Valencia, Spain</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Ignacio</namePart><namePart type="family">Blanquer</namePart><affiliation>Institute of Instrumentation for Molecular Imaging (I3M), Universitat Politècnica de València, València, Spain</affiliation><affiliation>Biomedical Imaging Research Group GIBI 230, Polytechnic University Hospital La Fe, Valencia, Spain</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="review-article" displayLabel="reviewArticle" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-L5L7X3NF-P">review-article</genre><originInfo><publisher>Wiley Periodicals, Inc.</publisher><place><placeTerm type="text">Hoboken, USA</placeTerm></place><dateIssued encoding="w3cdtf">2016-03</dateIssued><dateCreated encoding="w3cdtf">2015-11-30</dateCreated><dateCaptured encoding="w3cdtf">2015-07-02</dateCaptured><dateValid encoding="w3cdtf">2015-11-06</dateValid><copyrightDate encoding="w3cdtf">2016</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><note type="funding">Generalitat Valenciana - No. GRISOLIA/2013/013; 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