IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.
Identifieur interne : 000948 ( Ncbi/Curation ); précédent : 000947; suivant : 000949IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.
Auteurs : Yu Peng [Hong Kong] ; Henry C M. Leung ; S M Yiu ; Francis Y L. ChinSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- genetics : Bacteria.
- methods : Metagenomics, Sequence Analysis, DNA, Single-Cell Analysis.
- Algorithms, Genome, High-Throughput Nucleotide Sequencing.
Abstract
Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. However, both technologies suffer from the problem that sequencing depth of different regions of a genome or genomes from different species are highly uneven. Most existing genome assemblers usually have an assumption that sequencing depths are even. These assemblers fail to construct correct long contigs.
DOI: 10.1093/bioinformatics/bts174
PubMed: 22495754
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pubmed:22495754Le document en format XML
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Leung</name></author><author><name sortKey="Yiu, S M" sort="Yiu, S M" uniqKey="Yiu S" first="S M" last="Yiu">S M Yiu</name></author><author><name sortKey="Chin, Francis Y L" sort="Chin, Francis Y L" uniqKey="Chin F" first="Francis Y L" last="Chin">Francis Y L. 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Leung</name></author><author><name sortKey="Yiu, S M" sort="Yiu, S M" uniqKey="Yiu S" first="S M" last="Yiu">S M Yiu</name></author><author><name sortKey="Chin, Francis Y L" sort="Chin, Francis Y L" uniqKey="Chin F" first="Francis Y L" last="Chin">Francis Y L. Chin</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Bacteria (genetics)</term><term>Genome</term><term>High-Throughput Nucleotide Sequencing</term><term>Metagenomics (methods)</term><term>Sequence Analysis, DNA (methods)</term><term>Single-Cell Analysis (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN ()</term><term>Analyse sur cellule unique ()</term><term>Bactéries (génétique)</term><term>Génome</term><term>Métagénomique ()</term><term>Séquençage nucléotidique à haut débit</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Bactéries</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Metagenomics</term><term>Sequence Analysis, DNA</term><term>Single-Cell Analysis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Genome</term><term>High-Throughput Nucleotide Sequencing</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Analyse sur cellule unique</term><term>Génome</term><term>Métagénomique</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. However, both technologies suffer from the problem that sequencing depth of different regions of a genome or genomes from different species are highly uneven. Most existing genome assemblers usually have an assumption that sequencing depths are even. These assemblers fail to construct correct long contigs.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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