Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
Identifieur interne : 001601 ( Main/Exploration ); précédent : 001600; suivant : 001602Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
Auteurs : Li Song [États-Unis] ; Liliana Florea [États-Unis]Source :
- GigaScience [ 2047-217X ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
- génétique : ARN.
- Analyse de séquence d'ARN.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA.
- methods : Sequence Analysis, RNA.
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
Affiliations:
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type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Florea, Liliana" sort="Florea, Liliana" uniqKey="Florea L" first="Liliana" last="Florea">Liliana Florea</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Department of Computer Science, Johns Hopkins University, Baltimore, 21218 USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Johns Hopkins University, Baltimore</wicri:regionArea><placeName><settlement type="city">Baltimore</settlement><region type="state">Maryland</region></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="Aff2">McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205 USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore</wicri:regionArea><placeName><settlement type="city">Baltimore</settlement><region type="state">Maryland</region></placeName></affiliation></author></analytic><series><title level="j">GigaScience</title><idno type="eISSN">2047-217X</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>RNA (genetics)</term><term>Sequence Analysis, RNA (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN (génétique)</term><term>Analyse de séquence d'ARN ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ARN</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><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></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 Weese</name></author><author><name sortKey="Rausch, T" uniqKey="Rausch T">T Rausch</name></author><author><name sortKey="Reinert, K" uniqKey="Reinert K">K Reinert</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, D" uniqKey="Kim D">D Kim</name></author><author><name sortKey="Pertea, G" uniqKey="Pertea G">G Pertea</name></author><author><name sortKey="Trapnell, C" uniqKey="Trapnell C">C Trapnell</name></author><author><name sortKey="Pimentel, H" uniqKey="Pimentel H">H Pimentel</name></author><author><name sortKey="Kelley, R" uniqKey="Kelley R">R Kelley</name></author><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Walenz, B" uniqKey="Walenz B">B Walenz</name></author><author><name sortKey="Florea, L" uniqKey="Florea L">L Florea</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Haas, Bj" uniqKey="Haas B">BJ Haas</name></author><author><name sortKey="Papanicolaou, A" uniqKey="Papanicolaou A">A Papanicolaou</name></author><author><name sortKey="Yassour, M" uniqKey="Yassour M">M Yassour</name></author><author><name sortKey="Grabherr, M" uniqKey="Grabherr M">M Grabherr</name></author><author><name sortKey="Blood, Pd" uniqKey="Blood P">PD Blood</name></author><author><name sortKey="Bowden, J" uniqKey="Bowden J">J Bowden</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bankevich, A" uniqKey="Bankevich A">A Bankevich</name></author><author><name sortKey="Nurk, S" uniqKey="Nurk S">S Nurk</name></author><author><name sortKey="Antipov, D" uniqKey="Antipov D">D Antipov</name></author><author><name sortKey="Gurevich, Aa" uniqKey="Gurevich A">AA Gurevich</name></author><author><name sortKey="Dvorkin, M" uniqKey="Dvorkin 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sortKey="Song, Li" sort="Song, Li" uniqKey="Song L" first="Li" last="Song">Li Song</name></region><name sortKey="Florea, Liliana" sort="Florea, Liliana" uniqKey="Florea L" first="Liliana" last="Florea">Liliana Florea</name><name sortKey="Florea, Liliana" sort="Florea, Liliana" uniqKey="Florea L" first="Liliana" last="Florea">Liliana Florea</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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