ILP-based maximum likelihood genome scaffolding.
Identifieur interne : 000386 ( Main/Exploration ); précédent : 000385; suivant : 000387ILP-based maximum likelihood genome scaffolding.
Auteurs : James Lindsay ; Hamed Salooti ; Ion M Ndoiu ; Alex ZelikovskySource :
- BMC bioinformatics ; 2014.
English descriptors
- KwdEn :
- MESH :
Abstract
Interest in de novo genome assembly has been renewed in the past decade due to rapid advances in high-throughput sequencing (HTS) technologies which generate relatively short reads resulting in highly fragmented assemblies consisting of contigs. Additional long-range linkage information is typically used to orient, order, and link contigs into larger structures referred to as scaffolds. Due to library preparation artifacts and erroneous mapping of reads originating from repeats, scaffolding remains a challenging problem. In this paper, we provide a scalable scaffolding algorithm (SILP2) employing a maximum likelihood model capturing read mapping uncertainty and/or non-uniformity of contig coverage which is solved using integer linear programming. A Non-Serial Dynamic Programming (NSDP) paradigm is applied to render our algorithm useful in the processing of larger mammalian genomes. To compare scaffolding tools, we employ novel quantitative metrics in addition to the extant metrics in the field. We have also expanded the set of experiments to include scaffolding of low-complexity metagenomic samples.
DOI: 10.1186/1471-2105-15-S9-S9
PubMed: 25253180
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 000138
- to stream PubMed, to step Curation: 000138
- to stream PubMed, to step Checkpoint: 000168
- to stream Ncbi, to step Merge: 000C54
- to stream Ncbi, to step Curation: 000C54
- to stream Ncbi, to step Checkpoint: 000C54
- to stream Main, to step Merge: 000375
- to stream Main, to step Curation: 000386
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">ILP-based maximum likelihood genome scaffolding.</title>
<author><name sortKey="Lindsay, James" sort="Lindsay, James" uniqKey="Lindsay J" first="James" last="Lindsay">James Lindsay</name>
</author>
<author><name sortKey="Salooti, Hamed" sort="Salooti, Hamed" uniqKey="Salooti H" first="Hamed" last="Salooti">Hamed Salooti</name>
</author>
<author><name sortKey="M Ndoiu, Ion" sort="M Ndoiu, Ion" uniqKey="M Ndoiu I" first="Ion" last="M Ndoiu">Ion M Ndoiu</name>
</author>
<author><name sortKey="Zelikovsky, Alex" sort="Zelikovsky, Alex" uniqKey="Zelikovsky A" first="Alex" last="Zelikovsky">Alex Zelikovsky</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2014">2014</date>
<idno type="doi">10.1186/1471-2105-15-S9-S9</idno>
<idno type="RBID">pubmed:25253180</idno>
<idno type="pmid">25253180</idno>
<idno type="wicri:Area/PubMed/Corpus">000138</idno>
<idno type="wicri:Area/PubMed/Curation">000138</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000168</idno>
<idno type="wicri:Area/Ncbi/Merge">000C54</idno>
<idno type="wicri:Area/Ncbi/Curation">000C54</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000C54</idno>
<idno type="wicri:Area/Main/Merge">000375</idno>
<idno type="wicri:Area/Main/Curation">000386</idno>
<idno type="wicri:Area/Main/Exploration">000386</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">ILP-based maximum likelihood genome scaffolding.</title>
<author><name sortKey="Lindsay, James" sort="Lindsay, James" uniqKey="Lindsay J" first="James" last="Lindsay">James Lindsay</name>
</author>
<author><name sortKey="Salooti, Hamed" sort="Salooti, Hamed" uniqKey="Salooti H" first="Hamed" last="Salooti">Hamed Salooti</name>
</author>
<author><name sortKey="M Ndoiu, Ion" sort="M Ndoiu, Ion" uniqKey="M Ndoiu I" first="Ion" last="M Ndoiu">Ion M Ndoiu</name>
</author>
<author><name sortKey="Zelikovsky, Alex" sort="Zelikovsky, Alex" uniqKey="Zelikovsky A" first="Alex" last="Zelikovsky">Alex Zelikovsky</name>
</author>
</analytic>
<series><title level="j">BMC bioinformatics</title>
<idno type="e-ISSN">1471-2105</idno>
<imprint><date when="2014" type="published">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>Animals</term>
<term>Genome</term>
<term>Genomics (methods)</term>
<term>High-Throughput Nucleotide Sequencing (methods)</term>
<term>Humans</term>
<term>Likelihood Functions</term>
<term>Metagenomics (methods)</term>
<term>Probability</term>
<term>Programming, Linear</term>
<term>Sequence Analysis, DNA (methods)</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Metagenomics</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Animals</term>
<term>Genome</term>
<term>Humans</term>
<term>Likelihood Functions</term>
<term>Probability</term>
<term>Programming, Linear</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Interest in de novo genome assembly has been renewed in the past decade due to rapid advances in high-throughput sequencing (HTS) technologies which generate relatively short reads resulting in highly fragmented assemblies consisting of contigs. Additional long-range linkage information is typically used to orient, order, and link contigs into larger structures referred to as scaffolds. Due to library preparation artifacts and erroneous mapping of reads originating from repeats, scaffolding remains a challenging problem. In this paper, we provide a scalable scaffolding algorithm (SILP2) employing a maximum likelihood model capturing read mapping uncertainty and/or non-uniformity of contig coverage which is solved using integer linear programming. A Non-Serial Dynamic Programming (NSDP) paradigm is applied to render our algorithm useful in the processing of larger mammalian genomes. To compare scaffolding tools, we employ novel quantitative metrics in addition to the extant metrics in the field. We have also expanded the set of experiments to include scaffolding of low-complexity metagenomic samples.</div>
</front>
</TEI>
<affiliations><list></list>
<tree><noCountry><name sortKey="Lindsay, James" sort="Lindsay, James" uniqKey="Lindsay J" first="James" last="Lindsay">James Lindsay</name>
<name sortKey="M Ndoiu, Ion" sort="M Ndoiu, Ion" uniqKey="M Ndoiu I" first="Ion" last="M Ndoiu">Ion M Ndoiu</name>
<name sortKey="Salooti, Hamed" sort="Salooti, Hamed" uniqKey="Salooti H" first="Hamed" last="Salooti">Hamed Salooti</name>
<name sortKey="Zelikovsky, Alex" sort="Zelikovsky, Alex" uniqKey="Zelikovsky A" first="Alex" last="Zelikovsky">Alex Zelikovsky</name>
</noCountry>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Musique/explor/OperaV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000386 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000386 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Wicri/Musique |area= OperaV1 |flux= Main |étape= Exploration |type= RBID |clé= pubmed:25253180 |texte= ILP-based maximum likelihood genome scaffolding. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:25253180" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \ | NlmPubMed2Wicri -a OperaV1
This area was generated with Dilib version V0.6.21. |