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Title: BBMap: A Fast, Accurate, Splice-Aware Aligner

Alignment of reads is one of the primary computational tasks in bioinformatics. Of paramount importance to resequencing, alignment is also crucial to other areas - quality control, scaffolding, string-graph assembly, homology detection, assembly evaluation, error-correction, expression quantification, and even as a tool to evaluate other tools. An optimal aligner would greatly improve virtually any sequencing process, but optimal alignment is prohibitively expensive for gigabases of data. Here, we will present BBMap [1], a fast splice-aware aligner for short and long reads. We will demonstrate that BBMap has superior speed, sensitivity, and specificity to alternative high-throughput aligners bowtie2 [2], bwa [3], smalt, [4] GSNAP [5], and BLASR [6].
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Resource Relation:
Conference: 9th Annual Genomics of Energy & Environment Meeting, Walnut Creek, CA, March 17-20, 2014
Research Org:
Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
09 BIOMASS FUELS; 99 GENERAL AND MISCELLANEOUS bioinformatics, resequencing, quality control, short and long reads, high-throughput