Fiona: a parallel and automatic strategy for read error correction
Identifieur interne : 000258 ( France/Analysis ); précédent : 000257; suivant : 000259Fiona: a parallel and automatic strategy for read error correction
Auteurs : Marcel H. Schulz [Allemagne, États-Unis] ; David Weese [Allemagne] ; Manuel Holtgrewe [Allemagne] ; Viktoria Dimitrova [France] ; Sijia Niu [France] ; Knut Reinert [Allemagne] ; Hugues Richard [France]Source :
- Bioinformatics [ 1367-4803 ] ; 2014.
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- MESH :
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Abstract
Url:
DOI: 10.1093/bioinformatics/btu440
PubMed: 25161220
PubMed Central: 4147893
Affiliations:
- Allemagne, France, États-Unis
- Berlin, Pennsylvanie, Sarre (Land), Île-de-France
- Berlin, Paris, Pittsburgh, Sarrebruck
- Université Carnegie-Mellon, Université Pierre-et-Marie-Curie
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PMC:4147893Le document en format XML
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>High-Throughput Nucleotide Sequencing (methods)</term>
<term>INDEL Mutation</term>
<term>Sequence Analysis, DNA (methods)</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term>
<term>Analyse de séquence d'ADN ()</term>
<term>Mutation de type INDEL</term>
<term>Séquençage nucléotidique à haut débit ()</term>
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<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term>
<term>Sequence Analysis, DNA</term>
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<term>INDEL Mutation</term>
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<keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term>
<term>Analyse de séquence d'ADN</term>
<term>Mutation de type INDEL</term>
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<front><div type="abstract" xml:lang="en"><p><bold>Motivation:</bold>
Automatic error correction of high-throughput sequencing data can have a dramatic impact on the amount of usable base pairs and their quality. It has been shown that the performance of tasks such as <italic>de novo</italic>
genome assembly and SNP calling can be dramatically improved after read error correction. While a large number of methods specialized for correcting substitution errors as found in Illumina data exist, few methods for the correction of indel errors, common to technologies like 454 or Ion Torrent, have been proposed.</p>
<p><bold>Results</bold>
: We present Fiona, a new stand-alone read error–correction method. Fiona provides a new statistical approach for sequencing error detection and optimal error correction and estimates its parameters automatically. Fiona is able to correct substitution, insertion and deletion errors and can be applied to any sequencing technology. It uses an efficient implementation of the partial suffix array to detect read overlaps with different seed lengths in parallel. We tested Fiona on several real datasets from a variety of organisms with different read lengths and compared its performance with state-of-the-art methods. Fiona shows a constantly higher correction accuracy over a broad range of datasets from 454 and Ion Torrent sequencers, without compromise in speed.</p>
<p><bold>Conclusion</bold>
: Fiona is an accurate parameter-free read error–correction method that can be run on inexpensive hardware and can make use of multicore parallelization whenever available. Fiona was implemented using the SeqAn library for sequence analysis and is publicly available for download at <ext-link ext-link-type="uri" xlink:href="http://www.seqan.de/projects/fiona">http://www.seqan.de/projects/fiona</ext-link>
.</p>
<p><bold>Contact</bold>
: <email>mschulz@mmci.uni-saarland.de</email>
or <email>hugues.richard@upmc.fr</email>
</p>
<p><bold>Supplementary information:</bold>
<ext-link ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/lookup/suppl/doi:10.1093/bioinformatics/btu440/-/DC1">Supplementary data</ext-link>
are available at <italic>Bioinformatics</italic>
online.</p>
</div>
</front>
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<li>Pennsylvanie</li>
<li>Sarre (Land)</li>
<li>Île-de-France</li>
</region>
<settlement><li>Berlin</li>
<li>Paris</li>
<li>Pittsburgh</li>
<li>Sarrebruck</li>
</settlement>
<orgName><li>Université Carnegie-Mellon</li>
<li>Université Pierre-et-Marie-Curie</li>
</orgName>
</list>
<tree><country name="Allemagne"><region name="Sarre (Land)"><name sortKey="Schulz, Marcel H" sort="Schulz, Marcel H" uniqKey="Schulz M" first="Marcel H." last="Schulz">Marcel H. Schulz</name>
</region>
<name sortKey="Holtgrewe, Manuel" sort="Holtgrewe, Manuel" uniqKey="Holtgrewe M" first="Manuel" last="Holtgrewe">Manuel Holtgrewe</name>
<name sortKey="Reinert, Knut" sort="Reinert, Knut" uniqKey="Reinert K" first="Knut" last="Reinert">Knut Reinert</name>
<name sortKey="Weese, David" sort="Weese, David" uniqKey="Weese D" first="David" last="Weese">David Weese</name>
</country>
<country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Schulz, Marcel H" sort="Schulz, Marcel H" uniqKey="Schulz M" first="Marcel H." last="Schulz">Marcel H. Schulz</name>
</region>
</country>
<country name="France"><region name="Île-de-France"><name sortKey="Dimitrova, Viktoria" sort="Dimitrova, Viktoria" uniqKey="Dimitrova V" first="Viktoria" last="Dimitrova">Viktoria Dimitrova</name>
</region>
<name sortKey="Dimitrova, Viktoria" sort="Dimitrova, Viktoria" uniqKey="Dimitrova V" first="Viktoria" last="Dimitrova">Viktoria Dimitrova</name>
<name sortKey="Niu, Sijia" sort="Niu, Sijia" uniqKey="Niu S" first="Sijia" last="Niu">Sijia Niu</name>
<name sortKey="Niu, Sijia" sort="Niu, Sijia" uniqKey="Niu S" first="Sijia" last="Niu">Sijia Niu</name>
<name sortKey="Richard, Hugues" sort="Richard, Hugues" uniqKey="Richard H" first="Hugues" last="Richard">Hugues Richard</name>
<name sortKey="Richard, Hugues" sort="Richard, Hugues" uniqKey="Richard H" first="Hugues" last="Richard">Hugues Richard</name>
</country>
</tree>
</affiliations>
</record>
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