title: BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.
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.
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
authors.forename: Justin
authors.initials: J
authors.lastname: Chu
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
authors.forename: Sara
authors.initials: S
authors.lastname: Sadeghi
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
authors.forename: Anthony
authors.initials: A
authors.lastname: Raymond
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
authors.forename: Shaun D
authors.initials: SD
authors.lastname: Jackman
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
authors.forename: Ka Ming
authors.initials: KM
authors.lastname: Nip
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
authors.forename: Richard
authors.initials: R
authors.lastname: Mar
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
authors.forename: Hamid
authors.initials: H
authors.lastname: Mohamadi
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
authors.forename: Yaron S
authors.initials: YS
authors.lastname: Butterfield
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
authors.forename: A Gordon
authors.initials: AG
authors.lastname: Robertson
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.
authors.forename: Inanç
authors.initials: I
authors.lastname: Birol
mesh_terms: D000465:Algorithms; D000818:Animals; D006801:Humans; D051379:Mice; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software