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.
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