MersV1, PubMed, Curation, bibRecord, 001788

Lighter: fast and memory-efficient sequencing error correction without counting.

Identifieur interne : 001788 ( PubMed/Curation ); précédent : 001787; suivant : 001789

Lighter: fast and memory-efficient sequencing error correction without counting.

Auteurs : Li Song ; Liliana Florea ; Ben Langmead

Source :

Genome biology [ 1474-760X ] ; 2014.

RBID : pubmed:25398208

Descripteurs français

KwdFr :
- Analyse de séquence d'ADN, Biologie informatique, Contrôle de qualité, Humains, Logiciel, Séquençage nucléotidique à haut débit ().
MESH :
- Analyse de séquence d'ADN, Biologie informatique, Contrôle de qualité, Humains, Logiciel, Séquençage nucléotidique à haut débit.

English descriptors

KwdEn :
- Computational Biology, High-Throughput Nucleotide Sequencing (methods), Humans, Quality Control, Sequence Analysis, DNA, Software.
MESH :
- methods : High-Throughput Nucleotide Sequencing.
- Computational Biology, Humans, Quality Control, Sequence Analysis, DNA, Software.

Abstract

Lighter is a fast, memory-efficient tool for correcting sequencing errors. Lighter avoids counting k-mers. Instead, it uses a pair of Bloom filters, one holding a sample of the input k-mers and the other holding k-mers likely to be correct. As long as the sampling fraction is adjusted in inverse proportion to the depth of sequencing, Bloom filter size can be held constant while maintaining near-constant accuracy. Lighter is parallelized, uses no secondary storage, and is both faster and more memory-efficient than competing approaches while achieving comparable accuracy.

DOI: 10.1186/s13059-014-0509-9
PubMed: 25398208

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Le document en format XML

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<author><name sortKey="Florea, Liliana" sort="Florea, Liliana" uniqKey="Florea L" first="Liliana" last="Florea">Liliana Florea</name>
</author>
<author><name sortKey="Langmead, Ben" sort="Langmead, Ben" uniqKey="Langmead B" first="Ben" last="Langmead">Ben Langmead</name>
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<front><div type="abstract" xml:lang="en">Lighter is a fast, memory-efficient tool for correcting sequencing errors. Lighter avoids counting k-mers. Instead, it uses a pair of Bloom filters, one holding a sample of the input k-mers and the other holding k-mers likely to be correct. As long as the sampling fraction is adjusted in inverse proportion to the depth of sequencing, Bloom filter size can be held constant while maintaining near-constant accuracy. Lighter is parallelized, uses no secondary storage, and is both faster and more memory-efficient than competing approaches while achieving comparable accuracy.</div>
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Lighter: fast and memory-efficient sequencing error correction without counting.

Lighter: fast and memory-efficient sequencing error correction without counting.

Source :

Descripteurs français

English descriptors

Abstract

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