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Title: 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. Mon . "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 = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2014},
month = {3}
}

Conference:
Other availability
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