Nov 16, 2014

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

Genome Biology
Li SongBen 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.

Mentioned in this Paper

Severe Acute Respiratory Syndrome
Computer Programs and Programming
Sequencing
Sequence Determinations, DNA
High-Throughput Nucleotide Sequencing
Computational Molecular Biology

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