OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees
Identifieur interne : 000103 ( Main/Exploration ); précédent : 000102; suivant : 000104OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees
Auteurs : Song Gao [Singapour] ; Denis Bertrand [Singapour] ; Burton K. H. Chia [Singapour] ; Niranjan Nagarajan [Singapour]Source :
- Genome Biology [ 1474-7596 ] ; 2016.
Abstract
The assembly of large, repeat-rich eukaryotic genomes represents a significant challenge in genomics. While long-read technologies have made the high-quality assembly of small, microbial genomes increasingly feasible, data generation can be expensive for larger genomes. OPERA-LG is a scalable, exact algorithm for the scaffold assembly of large, repeat-rich genomes, out-performing state-of-the-art programs for scaffold correctness and contiguity. It provides a rigorous framework for scaffolding of repetitive sequences and a systematic approach for combining data from different second-generation and third-generation sequencing technologies. OPERA-LG provides an avenue for systematic augmentation and improvement of thousands of existing draft eukaryotic genome assemblies.
The online version of this article (doi:10.1186/s13059-016-0951-y) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13059-016-0951-y
PubMed: 27169502
PubMed Central: 4864936
Affiliations:
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H." last="Chia">Burton K. H. Chia</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672 Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Computational and Systems Biology, Genome Institute of Singapore, Singapore</wicri:regionArea><wicri:noRegion>Singapore</wicri:noRegion></affiliation></author><author><name sortKey="Nagarajan, Niranjan" sort="Nagarajan, Niranjan" uniqKey="Nagarajan N" first="Niranjan" last="Nagarajan">Niranjan Nagarajan</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672 Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Computational and Systems Biology, Genome Institute of Singapore, Singapore</wicri:regionArea><wicri:noRegion>Singapore</wicri:noRegion></affiliation></author></analytic><series><title level="j">Genome Biology</title><idno type="ISSN">1474-7596</idno><idno type="eISSN">1474-760X</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The assembly of large, repeat-rich eukaryotic genomes represents a significant challenge in genomics. While long-read technologies have made the high-quality assembly of small, microbial genomes increasingly feasible, data generation can be expensive for larger genomes. OPERA-LG is a scalable, exact algorithm for the scaffold assembly of large, repeat-rich genomes, out-performing state-of-the-art programs for scaffold correctness and contiguity. It provides a rigorous framework for scaffolding of repetitive sequences and a systematic approach for combining data from different second-generation and third-generation sequencing technologies. OPERA-LG provides an avenue for systematic augmentation and improvement of thousands of existing draft eukaryotic genome assemblies.</p><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13059-016-0951-y) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Kececioglu, Jd" uniqKey="Kececioglu J">JD Kececioglu</name></author><author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Medvedev, P" uniqKey="Medvedev P">P Medvedev</name></author><author><name sortKey="Georgiou, K" uniqKey="Georgiou K">K Georgiou</name></author><author><name sortKey="Myers, G" uniqKey="Myers G">G Myers</name></author><author><name sortKey="Brudno, M" uniqKey="Brudno M">M 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sortKey="Ho, I" uniqKey="Ho I">I Ho</name></author><author><name sortKey="Sunkara, S" uniqKey="Sunkara S">S Sunkara</name></author><author><name sortKey="Luo, S" uniqKey="Luo S">S Luo</name></author><author><name sortKey="Schroth, Gp" uniqKey="Schroth G">GP Schroth</name></author><author><name sortKey="Rokhsar, Ds" uniqKey="Rokhsar D">DS Rokhsar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hunt, M" uniqKey="Hunt M">M Hunt</name></author><author><name sortKey="Kikuchi, T" uniqKey="Kikuchi T">T Kikuchi</name></author><author><name sortKey="Sanders, M" uniqKey="Sanders M">M Sanders</name></author><author><name sortKey="Newbold, C" uniqKey="Newbold C">C Newbold</name></author><author><name sortKey="Berriman, M" uniqKey="Berriman M">M Berriman</name></author><author><name sortKey="Otto, Td" uniqKey="Otto T">TD Otto</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name></author><author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Singapour</li></country></list><tree><country name="Singapour"><noRegion><name sortKey="Gao, Song" sort="Gao, Song" uniqKey="Gao S" first="Song" last="Gao">Song Gao</name></noRegion><name sortKey="Bertrand, Denis" sort="Bertrand, Denis" uniqKey="Bertrand D" first="Denis" last="Bertrand">Denis Bertrand</name><name sortKey="Chia, Burton K H" sort="Chia, Burton K H" uniqKey="Chia B" first="Burton K. H." last="Chia">Burton K. H. Chia</name><name sortKey="Gao, Song" sort="Gao, Song" uniqKey="Gao S" first="Song" last="Gao">Song Gao</name><name sortKey="Nagarajan, Niranjan" sort="Nagarajan, Niranjan" uniqKey="Nagarajan N" first="Niranjan" last="Nagarajan">Niranjan Nagarajan</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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