Lighter: fast and memory-efficient sequencing error correction without counting View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-11

AUTHORS

Li Song, Liliana Florea, Ben Langmead

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. More... »

PAGES

509

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13059-014-0509-9

DOI

http://dx.doi.org/10.1186/s13059-014-0509-9

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1016075758

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/25398208


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