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Bioinformatics. 2014 Dec 1;30(23):3402-4. doi: 10.1093/bioinformatics/btu558. Epub 2014 Aug 20.

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.

Author information

1
Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.

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.

PMID:
25143290
PMCID:
PMC4816029
DOI:
10.1093/bioinformatics/btu558
[Indexed for MEDLINE]
Free PMC Article

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