BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 25143290.
- Also identified by DOI 10.1093/bioinformatics/btu558 and PMC identifier 4816029.
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Abstract
Large datasets can be screened for sequences from a specific organism, quickly and with low memory requirements, by a data structure that supports time- and memory-efficient set membership queries. Bloom filters offer such queries but require that false positives be controlled. We present BioBloom Tools, a Bloom filter-based sequence-screening tool that is faster than BWA, Bowtie 2 (popular alignment algorithms) and FACS (a membership query algorithm). It delivers accuracies comparable with these tools, controls false positives and has low memory requirements. Availability and implementaion: www.bcgsc.ca/platform/bioinfo/software/biobloomtools.
Medical subject headings
- Sequence Analysis, DNA
- Software