Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly
Identifieur interne : 001478 ( Ncbi/Checkpoint ); précédent : 001477; suivant : 001479Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly
Auteurs : Katrin Sameith [Allemagne] ; Juliana G. Roscito [Allemagne] ; Michael Hiller [Allemagne]Source :
- Briefings in Bioinformatics [ 1467-5463 ] ; 2016.
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Abstract
Next-generation sequencers such as Illumina can now produce reads up to 300 bp with high throughput, which is attractive for genome assembly. A first step in genome assembly is to computationally correct sequencing errors. However, correcting all errors in these longer reads is challenging. Here, we show that reads with remaining errors after correction often overlap repeats, where short erroneous
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DOI: 10.1093/bib/bbw003
PubMed: 26868358
PubMed Central: 5221426
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Roscito</name><affiliation wicri:level="3"><nlm:aff id="AFF1">Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute of Molecular Cell Biology and Genetics, Dresden</wicri:regionArea><placeName><region type="land" nuts="1">Saxe (Land)</region><region type="district" nuts="2">District de Dresde</region><settlement type="city">Dresde</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="AFF2">Max Planck Institute for the Physics of Complex Systems, Dresden, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for the Physics of Complex Systems, Dresden</wicri:regionArea><placeName><region type="land" nuts="1">Saxe (Land)</region><region type="district" nuts="2">District de Dresde</region><settlement type="city">Dresde</settlement></placeName></affiliation></author><author><name sortKey="Hiller, Michael" sort="Hiller, Michael" uniqKey="Hiller M" first="Michael" last="Hiller">Michael Hiller</name><affiliation wicri:level="3"><nlm:aff id="AFF1">Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute of Molecular Cell Biology and Genetics, Dresden</wicri:regionArea><placeName><region type="land" nuts="1">Saxe (Land)</region><region type="district" nuts="2">District de Dresde</region><settlement type="city">Dresde</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="AFF2">Max Planck Institute for the Physics of Complex Systems, Dresden, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for the Physics of Complex Systems, Dresden</wicri:regionArea><placeName><region type="land" nuts="1">Saxe (Land)</region><region type="district" nuts="2">District de Dresde</region><settlement type="city">Dresde</settlement></placeName></affiliation></author></analytic><series><title level="j">Briefings in Bioinformatics</title><idno type="ISSN">1467-5463</idno><idno type="eISSN">1477-4054</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>High-Throughput Nucleotide Sequencing</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Séquençage nucléotidique à haut débit</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>High-Throughput Nucleotide Sequencing</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>Next-generation sequencers such as Illumina can now produce reads up to 300 bp with high throughput, which is attractive for genome assembly. A first step in genome assembly is to computationally correct sequencing errors. However, correcting all errors in these longer reads is challenging. Here, we show that reads with remaining errors after correction often overlap repeats, where short erroneous <italic>k</italic>-mers occur in other copies of the repeat. We developed an iterative error correction pipeline that runs the previously published String Graph Assembler (SGA) in multiple rounds of <italic>k</italic>-mer-based correction with an increasing <italic>k</italic>-mer size, followed by a final round of overlap-based correction. By combining the advantages of small and large <italic>k</italic>-mers, this approach corrects more errors in repeats and minimizes the total amount of erroneous reads. We show that higher read accuracy increases contig lengths two to three times. We provide SGA-Iteratively Correcting Errors (<ext-link ext-link-type="uri" xlink:href="https://github.com/hillerlab/IterativeErrorCorrection/">https://github.com/hillerlab/IterativeErrorCorrection/</ext-link>) that implements iterative error correction by using modules from SGA.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Laehnemann, D" uniqKey="Laehnemann D">D Laehnemann</name></author><author><name sortKey="Borkhardt, A" uniqKey="Borkhardt A">A Borkhardt</name></author><author><name sortKey="Mchardy, Ac" uniqKey="Mchardy A">AC McHardy</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="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 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Pan</name></author><author><name sortKey="Hu, L" uniqKey="Hu L">L Hu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hu, X" uniqKey="Hu X">X Hu</name></author><author><name sortKey="Yuan, J" uniqKey="Yuan J">J Yuan</name></author><author><name sortKey="Shi, Y" uniqKey="Shi Y">Y Shi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huang, W" uniqKey="Huang W">W Huang</name></author><author><name sortKey="Li, L" uniqKey="Li L">L Li</name></author><author><name sortKey="Myers, Jr" uniqKey="Myers J">JR Myers</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rosenbloom, Kr" uniqKey="Rosenbloom K">KR Rosenbloom</name></author><author><name sortKey="Armstrong, J" uniqKey="Armstrong J">J Armstrong</name></author><author><name sortKey="Barber, Gp" uniqKey="Barber G">GP Barber</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Simpson, Jt" uniqKey="Simpson J">JT Simpson</name></author><author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Langmead, B" uniqKey="Langmead B">B Langmead</name></author><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Simao, Fa" uniqKey="Simao F">FA Simão</name></author><author><name sortKey="Waterhouse, Rm" uniqKey="Waterhouse R">RM Waterhouse</name></author><author><name sortKey="Ioannidis, P" uniqKey="Ioannidis P">P Ioannidis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Treangen, Tj" uniqKey="Treangen T">TJ Treangen</name></author><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li></country><region><li>District de Dresde</li><li>Saxe (Land)</li></region><settlement><li>Dresde</li></settlement></list><tree><country name="Allemagne"><region name="Saxe (Land)"><name sortKey="Sameith, Katrin" sort="Sameith, Katrin" uniqKey="Sameith K" first="Katrin" last="Sameith">Katrin Sameith</name></region><name sortKey="Hiller, Michael" sort="Hiller, Michael" uniqKey="Hiller M" first="Michael" last="Hiller">Michael Hiller</name><name sortKey="Hiller, Michael" sort="Hiller, Michael" uniqKey="Hiller M" first="Michael" last="Hiller">Michael Hiller</name><name sortKey="Roscito, Juliana G" sort="Roscito, Juliana G" uniqKey="Roscito J" first="Juliana G" last="Roscito">Juliana G. Roscito</name><name sortKey="Roscito, Juliana G" sort="Roscito, Juliana G" uniqKey="Roscito J" first="Juliana G" last="Roscito">Juliana G. Roscito</name><name sortKey="Sameith, Katrin" sort="Sameith, Katrin" uniqKey="Sameith K" first="Katrin" last="Sameith">Katrin Sameith</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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