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Title: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper (BELLA) v1.0

Abstract

BELLA is a long-read overlapper and read-to-read aligner that exploits novel approaches for selecting reliable k-mer seeds for filtering and for detecting overlapping read pairs to reconstruct the whole genome. BELLA uses a sparse matrix-matrix multiplication for high-performance overlap detection and then performs pairwise alignment on the overlapping read pairs. BELLA can be built with different pre-existing aligners to use on each read pair, so precision rates are determined by those aligners. Our evaluations include real and synthetic datasets with varying size and complexity and include recall, precision, and running time. BELLA's overlap detection retains nearly all true alignments, with recall rates that exceed other aligners, yet it filters enough read pairs that the running time, including pairwise alignments, is closer to tools that only perform overlapping and is significantly faster than tools that also perform alignment

Authors:
; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1467871
Alternate Identifier(s):
17092
Report Number(s):
BELLA v1.0
DOE Contract Number:  
AC02-05CH11231
Resource Type:
Software
Open Source:
Yes
Source Code Available:
No
Country of Publication:
United States

Citation Formats

Guidi, Giulia, Ellis, Marquita, Buluc, Aydin, and USDOE. Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper (BELLA) v1.0. Computer software. https://www.osti.gov//servlets/purl/1467871. USDOE. 9 May. 2018. Web. doi:10.11578/dc.20180831.1.
Guidi, Giulia, Ellis, Marquita, Buluc, Aydin, & USDOE. (2018, May 9). Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper (BELLA) v1.0 [Computer software]. https://www.osti.gov//servlets/purl/1467871. doi:10.11578/dc.20180831.1.
Guidi, Giulia, Ellis, Marquita, Buluc, Aydin, and USDOE. Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper (BELLA) v1.0. Computer software. May 9, 2018. https://www.osti.gov//servlets/purl/1467871. doi:10.11578/dc.20180831.1.
@misc{osti_1467871,
title = {Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper (BELLA) v1.0},
author = {Guidi, Giulia and Ellis, Marquita and Buluc, Aydin and USDOE},
abstractNote = {BELLA is a long-read overlapper and read-to-read aligner that exploits novel approaches for selecting reliable k-mer seeds for filtering and for detecting overlapping read pairs to reconstruct the whole genome. BELLA uses a sparse matrix-matrix multiplication for high-performance overlap detection and then performs pairwise alignment on the overlapping read pairs. BELLA can be built with different pre-existing aligners to use on each read pair, so precision rates are determined by those aligners. Our evaluations include real and synthetic datasets with varying size and complexity and include recall, precision, and running time. BELLA's overlap detection retains nearly all true alignments, with recall rates that exceed other aligners, yet it filters enough read pairs that the running time, including pairwise alignments, is closer to tools that only perform overlapping and is significantly faster than tools that also perform alignment},
url = {https://www.osti.gov//servlets/purl/1467871},
doi = {10.11578/dc.20180831.1},
year = {2018},
month = {5},
note =
}

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