Improving Bloom Filter Performance on Sequence Data Using k-mer Bloom Filters.

ABSTRACT: Using a sequence's k-mer content rather than the full sequence directly has enabled significant performance improvements in several sequencing applications, such as metagenomic species identification, estimation of transcript abundances, and alignment-free comparison of sequencing data. As k-mer sets often reach hundreds of millions of elements, traditional data structures are often impractical for k-mer set storage, and Bloom filters (BFs) and their variants are used instead. BFs reduce the memory footprint required to store millions of k-mers while allowing for fast set containment queries, at the cost of a low false positive rate (FPR). We show that, because k-mers are derived from sequencing reads, the information about k-mer overlap in the original sequence can be used to reduce the F

SUBMITTER: Pellow D 

PROVIDER: S-EPMC5467106 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature