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

Li Song, Liliana D Florea, Ben Langmead

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)509
Number of pages1
JournalGenome Biology
Volume15
Issue number11
StatePublished - 2014
Externally publishedYes

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ASJC Scopus subject areas

  • Medicine(all)

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