Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
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Auteurs : Li Song [États-Unis] ; Liliana Florea [États-Unis]Source :
- GigaScience [ 2047-217X ] ; 2015.
Abstract
Next-generation sequencing of cellular RNA (RNA-seq) is rapidly becoming the cornerstone of transcriptomic analysis. However, sequencing errors in the already short RNA-seq reads complicate bioinformatics analyses, in particular alignment and assembly. Error correction methods have been highly effective for whole-genome sequencing (WGS) reads, but are unsuitable for RNA-seq reads, owing to the variation in gene expression levels and alternative splicing.
We developed a
Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run on virtually any desktop or server. The software is available free of charge under the GNU General Public License from
The online version of this article (doi:10.1186/s13742-015-0089-y) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13742-015-0089-y
PubMed: 26500767
PubMed Central: 4615873
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However, sequencing errors in the already short RNA-seq reads complicate bioinformatics analyses, in particular alignment and assembly. Error correction methods have been highly effective for whole-genome sequencing (WGS) reads, but are unsuitable for RNA-seq reads, owing to the variation in gene expression levels and alternative splicing.</p></sec><sec><title>Findings</title><p>We developed a <italic>k</italic>-mer based method, Rcorrector, to correct random sequencing errors in Illumina RNA-seq reads. Rcorrector uses a De Bruijn graph to compactly represent all trusted <italic>k</italic>-mers in the input reads. Unlike WGS read correctors, which use a global threshold to determine trusted <italic>k</italic>-mers, Rcorrector computes a local threshold at every position in a read.</p></sec><sec><title>Conclusions</title><p>Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run on virtually any desktop or server. The software is available free of charge under the GNU General Public License from <ext-link ext-link-type="uri" xlink:href="https://github.com/mourisl/Rcorrector/">https://github.com/mourisl/Rcorrector/</ext-link>.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13742-015-0089-y) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Heo, Y" uniqKey="Heo Y">Y Heo</name></author><author><name sortKey="Wu, Xl" uniqKey="Wu X">XL Wu</name></author><author><name sortKey="Chen, D" uniqKey="Chen D">D Chen</name></author><author><name sortKey="Ma, J" uniqKey="Ma J">J Ma</name></author><author><name sortKey="Hwu, Wm" uniqKey="Hwu W">WM Hwu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Song, L" uniqKey="Song L">L Song</name></author><author><name sortKey="Florea, L" uniqKey="Florea L">L Florea</name></author><author><name sortKey="Langmead, B" uniqKey="Langmead B">B Langmead</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, X" uniqKey="Yang X">X Yang</name></author><author><name sortKey="Chockalingam, Sp" uniqKey="Chockalingam S">SP Chockalingam</name></author><author><name sortKey="Aluru, S" uniqKey="Aluru S">S Aluru</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kelley, D" uniqKey="Kelley D">D Kelley</name></author><author><name sortKey="Schatz, M" uniqKey="Schatz M">M Schatz</name></author><author><name sortKey="Salzberg, S" uniqKey="Salzberg S">S Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Medvedev, P" uniqKey="Medvedev P">P Medvedev</name></author><author><name sortKey="Scott, E" uniqKey="Scott E">E Scott</name></author><author><name sortKey="Kakaradov, B" uniqKey="Kakaradov B">B Kakaradov</name></author><author><name sortKey="Pevzner, P" uniqKey="Pevzner P">P Pevzner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y Liu</name></author><author><name sortKey="Schroder, J" uniqKey="Schroder J">J Schröder</name></author><author><name sortKey="Schmidt, B" uniqKey="Schmidt B">B Schmidt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schroder, J" uniqKey="Schroder J">J Schröder</name></author><author><name sortKey="Schroder, H" uniqKey="Schroder H">H Schröder</name></author><author><name sortKey="Puglisi, Sj" uniqKey="Puglisi S">SJ Puglisi</name></author><author><name sortKey="Sinha, R" uniqKey="Sinha R">R Sinha</name></author><author><name sortKey="Schmidt, B" uniqKey="Schmidt B">B Schmidt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Salmela, L" uniqKey="Salmela L">L Salmela</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ilie, L" uniqKey="Ilie L">L Ilie</name></author><author><name sortKey="Fazayeli, F" uniqKey="Fazayeli F">F Fazayeli</name></author><author><name sortKey="Ilie, S" uniqKey="Ilie S">S Ilie</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Salmela, L" uniqKey="Salmela L">L Salmela</name></author><author><name sortKey="Schroder, J" uniqKey="Schroder J">J Schröder</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Le, Hs" uniqKey="Le H">HS Le</name></author><author><name sortKey="Schulz, Mh" uniqKey="Schulz M">MH Schulz</name></author><author><name sortKey="Mccauley, Bm" uniqKey="Mccauley B">BM McCauley</name></author><author><name sortKey="Hinman, Vf" uniqKey="Hinman V">VF Hinman</name></author><author><name sortKey="Bar Joseph, Z" uniqKey="Bar Joseph Z">Z Bar-Joseph</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Marcais, G" uniqKey="Marcais G">G Marçais</name></author><author><name sortKey="Kingsford, C" uniqKey="Kingsford C">C Kingsford</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Griebel, T" uniqKey="Griebel T">T Griebel</name></author><author><name sortKey="Zacher, B" uniqKey="Zacher B">B Zacher</name></author><author><name sortKey="Ribeca, P" uniqKey="Ribeca P">P Ribeca</name></author><author><name sortKey="Raineri, E" uniqKey="Raineri E">E Raineri</name></author><author><name sortKey="Lacroix, V" uniqKey="Lacroix V">V Lacroix</name></author><author><name sortKey="Guig, R" uniqKey="Guig R">R Guigó</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Doring, A" uniqKey="Doring A">A Doring</name></author><author><name sortKey="Weese, D" uniqKey="Weese D">D 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Gigascience</journal-id><journal-id journal-id-type="iso-abbrev">Gigascience</journal-id><journal-title-group><journal-title>GigaScience</journal-title></journal-title-group><issn pub-type="epub">2047-217X</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26500767</article-id><article-id pub-id-type="pmc">4615873</article-id><article-id pub-id-type="publisher-id">89</article-id><article-id pub-id-type="doi">10.1186/s13742-015-0089-y</article-id><article-categories><subj-group subj-group-type="heading"><subject>Technical Note</subject></subj-group></article-categories><title-group><article-title>Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Song</surname><given-names>Li</given-names></name><address><email>lsong10@jhu.edu</email></address><xref ref-type="aff" rid="Aff1">1</xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Florea</surname><given-names>Liliana</given-names></name><address><email>florea@jhu.edu</email></address><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff2">2</xref></contrib><aff id="Aff1"><label>1</label>Department of Computer Science, Johns Hopkins University, Baltimore, 21218 USA</aff><aff id="Aff2"><label>2</label>McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205 USA</aff></contrib-group><pub-date pub-type="epub"><day>19</day><month>10</month><year>2015</year></pub-date><pub-date pub-type="pmc-release"><day>19</day><month>10</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>4</volume><elocation-id>48</elocation-id><history><date date-type="received"><day>1</day><month>6</month><year>2015</year></date><date date-type="accepted"><day>9</day><month>10</month><year>2015</year></date></history><permissions><copyright-statement>© Song and Florea. 2015</copyright-statement><license license-type="OpenAccess"><license-p><bold>Open Access</bold> This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><abstract id="Abs1"><sec><title>Background</title><p>Next-generation sequencing of cellular RNA (RNA-seq) is rapidly becoming the cornerstone of transcriptomic analysis. However, sequencing errors in the already short RNA-seq reads complicate bioinformatics analyses, in particular alignment and assembly. Error correction methods have been highly effective for whole-genome sequencing (WGS) reads, but are unsuitable for RNA-seq reads, owing to the variation in gene expression levels and alternative splicing.</p></sec><sec><title>Findings</title><p>We developed a <italic>k</italic>-mer based method, Rcorrector, to correct random sequencing errors in Illumina RNA-seq reads. Rcorrector uses a De Bruijn graph to compactly represent all trusted <italic>k</italic>-mers in the input reads. Unlike WGS read correctors, which use a global threshold to determine trusted <italic>k</italic>-mers, Rcorrector computes a local threshold at every position in a read.</p></sec><sec><title>Conclusions</title><p>Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run on virtually any desktop or server. The software is available free of charge under the GNU General Public License from <ext-link ext-link-type="uri" xlink:href="https://github.com/mourisl/Rcorrector/">https://github.com/mourisl/Rcorrector/</ext-link>.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13742-015-0089-y) contains supplementary material, which is available to authorized users.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>Next-generation sequencing</kwd><kwd>RNA-seq</kwd><kwd>Error correction</kwd><kwd><italic>k</italic>-mers</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2015</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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