Lighter: fast and memory-efficient sequencing error correction without counting
Identifieur interne : 001B97 ( Main/Curation ); précédent : 001B96; suivant : 001B98Lighter: fast and memory-efficient sequencing error correction without counting
Auteurs : Li Song [États-Unis] ; Liliana Florea [États-Unis] ; Ben Langmead [États-Unis]Source :
- Genome Biology [ 1465-6906 ] ; 2014.
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Abstract
Lighter is a fast, memory-efficient tool for correcting sequencing errors. Lighter avoids counting
The online version of this article (doi:10.1186/s13059-014-0509-9) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13059-014-0509-9
PubMed: 25398208
PubMed Central: 4248469
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PMC:4248469Le document en format XML
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<front><div type="abstract" xml:lang="en"><p>Lighter is a fast, memory-efficient tool for correcting sequencing errors. Lighter avoids counting <italic>k</italic>
-mers. Instead, it uses a pair of Bloom filters, one holding a sample of the input <italic>k</italic>
-mers and the other holding <italic>k</italic>
-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.</p>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s13059-014-0509-9) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
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<author><name sortKey="Pop, M" uniqKey="Pop M">M Pop</name>
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<author><name sortKey="Almeida, J" uniqKey="Almeida J">J Almeida</name>
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<author><name sortKey="Medvedev, P" uniqKey="Medvedev P">P Medvedev</name>
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