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Lighter: fast and memory-efficient error correction without counting

By Li Song, Liliana Florea, Ben Langmead

Posted 27 May 2014
bioRxiv DOI: 10.1101/005579 (published DOI: 10.1186/s13059-014-0509-9)

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.

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