U.S. Department of EnergyOffice of Scientific and Technical Information
BBMap: A Fast, Accurate, Splice-Aware Aligner
Abstract
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].
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1241166
- Report Number(s):
- LBNL-7065E
- DOE Contract Number:
- DE-AC02-05CH11231
- Resource Type:
- Conference
- Resource Relation:
- Conference: 9th Annual Genomics of Energy & Environment Meeting, Walnut Creek, CA, March 17-20, 2014
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 09 BIOMASS FUELS; 99 GENERAL AND MISCELLANEOUS; bioinformatics, resequencing, quality control, short and long reads, high-throughput
Citation Formats
Bushnell, Brian. BBMap: A Fast, Accurate, Splice-Aware Aligner. United States: N. p., 2014.
Web.
Bushnell, Brian. BBMap: A Fast, Accurate, Splice-Aware Aligner. United States.
Bushnell, Brian. 2014.
"BBMap: A Fast, Accurate, Splice-Aware Aligner". United States. https://www.osti.gov/servlets/purl/1241166.
@article{osti_1241166,
title = {BBMap: A Fast, Accurate, Splice-Aware Aligner},
author = {Bushnell, Brian},
abstractNote = {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].},
doi = {},
url = {https://www.osti.gov/biblio/1241166},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2014},
month = {3}
}