BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.
BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.
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DOI：
10.1093/bioinformatics/btu558
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发表时间：
2014-12-01
期刊：
影响因子：
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通讯作者：
Birol I
中科院分区：
文献类型：
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作者：
Chu J;Sadeghi S;Raymond A;Jackman SD;Nip KM;Mar R;Mohamadi H;Butterfield YS;Robertson AG;Birol I
通过一种支持高效利用时间和内存进行集合成员查询的数据结构，可以快速且在低内存需求的情况下，针对特定生物体的序列对大型数据集进行筛选。布隆过滤器可提供此类查询，但需要对误报进行控制。我们介绍BioBloom Tools，这是一种基于布隆过滤器的序列筛选工具，它比BWA、Bowtie 2（常用的比对算法）和FACS（一种成员查询算法）速度更快。它能提供与这些工具相当的准确性，可控制误报且内存需求低。
可用性和实现：www.bcgsc.ca/platform/bioinfo/software/biobloomtools
联系人：cjustin@bcgsc.ca或ibirol@bcgsc.ca
补充信息：补充数据可在《生物信息学》在线获取。
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 Contact: cjustin@bcgsc.ca or ibirol@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online.