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

https://academic.oup.com/bioinformatics/article/30/23/3402/207237
 

Justin Chu Sara Sadeghi Anthony Raymond Shaun D. Jackman Ka Ming NipRichard Mar Hamid Mohamadi Yaron S. Butterfield A. Gordon Robertson Inanç Birol

Bioinformatics, Volume 30, Issue 23, 1 December 2014, Pages 3402–3404,https://doi.org/10.1093/bioinformatics/btu558

Published:

 

20 August 2014

 

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