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- Title
BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.
- Authors
Chu, Justin; Sadeghi, Sara; Raymond, Anthony; Jackman, Shaun D.; Nip, Ka Ming; Mar, Richard; Mohamadi, Hamid; Butterfield, Yaron S.; Robertson, A. Gordon; Birol, Inanç
- 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/biobloomtoolsContact: cjustin@bcgsc.ca or ibirol@bcgsc.caSupplementary information: Supplementary data are available at Bioinformatics online.
- Subjects
NUCLEOTIDE sequencing; BOW-tie antennas; GENETIC techniques; COMPUTER algorithms; SEQUENCE alignment
- Publication
Bioinformatics, 2014, Vol 30, Issue 23, p3402
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btu558