LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads.
Identifieur interne : 001177 ( Main/Exploration ); précédent : 001176; suivant : 001178LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads.
Auteurs : Sara El-Metwally [Égypte] ; Magdi Zakaria [Égypte] ; Taher Hamza [Égypte]Source :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
Abstract
The deluge of current sequenced data has exceeded Moore's Law, more than doubling every 2 years since the next-generation sequencing (NGS) technologies were invented. Accordingly, we will able to generate more and more data with high speed at fixed cost, but lack the computational resources to store, process and analyze it. With error prone high throughput NGS reads and genomic repeats, the assembly graph contains massive amount of redundant nodes and branching edges. Most assembly pipelines require this large graph to reside in memory to start their workflows, which is intractable for mammalian genomes. Resource-efficient genome assemblers combine both the power of advanced computing techniques and innovative data structures to encode the assembly graph efficiently in a computer memory.
DOI: 10.1093/bioinformatics/btw470
PubMed: 27412092
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 000F22
- to stream PubMed, to step Curation: 000F22
- to stream PubMed, to step Checkpoint: 001029
- to stream Ncbi, to step Merge: 001699
- to stream Ncbi, to step Curation: 001699
- to stream Ncbi, to step Checkpoint: 001699
- to stream Main, to step Merge: 001181
- to stream Main, to step Curation: 001177
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads.</title><author><name sortKey="El Metwally, Sara" sort="El Metwally, Sara" uniqKey="El Metwally S" first="Sara" last="El-Metwally">Sara El-Metwally</name><affiliation wicri:level="4"><nlm:affiliation>Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura 35516, Egypt.</nlm:affiliation><country xml:lang="fr">Égypte</country><wicri:regionArea>Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura 35516</wicri:regionArea><orgName type="university">Université de Californie du Sud</orgName><placeName><settlement type="city">Los Angeles</settlement><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Zakaria, Magdi" sort="Zakaria, Magdi" uniqKey="Zakaria M" first="Magdi" last="Zakaria">Magdi Zakaria</name><affiliation wicri:level="1"><nlm:affiliation>Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura 35516, Egypt.</nlm:affiliation><country xml:lang="fr">Égypte</country><wicri:regionArea>Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura 35516</wicri:regionArea><wicri:noRegion>Mansoura 35516</wicri:noRegion></affiliation></author><author><name sortKey="Hamza, Taher" sort="Hamza, Taher" uniqKey="Hamza T" first="Taher" last="Hamza">Taher Hamza</name><affiliation wicri:level="1"><nlm:affiliation>Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura 35516, Egypt.</nlm:affiliation><country xml:lang="fr">Égypte</country><wicri:regionArea>Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura 35516</wicri:regionArea><wicri:noRegion>Mansoura 35516</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:27412092</idno><idno type="pmid">27412092</idno><idno type="doi">10.1093/bioinformatics/btw470</idno><idno type="wicri:Area/PubMed/Corpus">000F22</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000F22</idno><idno type="wicri:Area/PubMed/Curation">000F22</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000F22</idno><idno type="wicri:Area/PubMed/Checkpoint">001029</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001029</idno><idno type="wicri:Area/Ncbi/Merge">001699</idno><idno type="wicri:Area/Ncbi/Curation">001699</idno><idno type="wicri:Area/Ncbi/Checkpoint">001699</idno><idno type="wicri:Area/Main/Merge">001181</idno><idno type="wicri:Area/Main/Curation">001177</idno><idno type="wicri:Area/Main/Exploration">001177</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads.</title><author><name sortKey="El Metwally, Sara" sort="El Metwally, Sara" uniqKey="El Metwally S" first="Sara" last="El-Metwally">Sara El-Metwally</name><affiliation wicri:level="4"><nlm:affiliation>Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura 35516, Egypt.</nlm:affiliation><country xml:lang="fr">Égypte</country><wicri:regionArea>Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura 35516</wicri:regionArea><orgName type="university">Université de Californie du Sud</orgName><placeName><settlement type="city">Los Angeles</settlement><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Zakaria, Magdi" sort="Zakaria, Magdi" uniqKey="Zakaria M" first="Magdi" last="Zakaria">Magdi Zakaria</name><affiliation wicri:level="1"><nlm:affiliation>Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura 35516, Egypt.</nlm:affiliation><country xml:lang="fr">Égypte</country><wicri:regionArea>Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura 35516</wicri:regionArea><wicri:noRegion>Mansoura 35516</wicri:noRegion></affiliation></author><author><name sortKey="Hamza, Taher" sort="Hamza, Taher" uniqKey="Hamza T" first="Taher" last="Hamza">Taher Hamza</name><affiliation wicri:level="1"><nlm:affiliation>Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura 35516, Egypt.</nlm:affiliation><country xml:lang="fr">Égypte</country><wicri:regionArea>Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura 35516</wicri:regionArea><wicri:noRegion>Mansoura 35516</wicri:noRegion></affiliation></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2016" type="published">2016</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</term><term>High-Throughput Nucleotide Sequencing (methods)</term><term>Humans</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Génome</term><term>Génomique</term><term>Humains</term><term>Séquençage nucléotidique à haut débit ()</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Genome</term><term>Genomics</term><term>Humans</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Génome</term><term>Génomique</term><term>Humains</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The deluge of current sequenced data has exceeded Moore's Law, more than doubling every 2 years since the next-generation sequencing (NGS) technologies were invented. Accordingly, we will able to generate more and more data with high speed at fixed cost, but lack the computational resources to store, process and analyze it. With error prone high throughput NGS reads and genomic repeats, the assembly graph contains massive amount of redundant nodes and branching edges. Most assembly pipelines require this large graph to reside in memory to start their workflows, which is intractable for mammalian genomes. Resource-efficient genome assemblers combine both the power of advanced computing techniques and innovative data structures to encode the assembly graph efficiently in a computer memory.</div></front></TEI><affiliations><list><country><li>Égypte</li></country><region><li>Californie</li></region><settlement><li>Los Angeles</li></settlement><orgName><li>Université de Californie du Sud</li></orgName></list><tree><country name="Égypte"><region name="Californie"><name sortKey="El Metwally, Sara" sort="El Metwally, Sara" uniqKey="El Metwally S" first="Sara" last="El-Metwally">Sara El-Metwally</name></region><name sortKey="Hamza, Taher" sort="Hamza, Taher" uniqKey="Hamza T" first="Taher" last="Hamza">Taher Hamza</name><name sortKey="Zakaria, Magdi" sort="Zakaria, Magdi" uniqKey="Zakaria M" first="Magdi" last="Zakaria">Magdi Zakaria</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001177 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 001177 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:27412092
|texte= LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:27412092" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |