BBMap: A Fast, Accurate, Splice-Aware Aligner

Conference · Mon Mar 17 04:00:00 EDT 2014

OSTI ID:1241166

Bushnell, Brian

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].

• Research Organization: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
• Sponsoring Organization: USDOE Office of Science (SC)
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 1241166
• Report Number(s): LBNL-7065E
• Country of Publication: United States
• Language: English

Related Subjects

09 BIOMASS FUELS
99 GENERAL AND MISCELLANEOUS
bioinformatics
resequencing
quality control
short and long reads
high-throughput