BiConstruct specifications

Information


Unique identifier OMICS_33816
Name BiConstruct
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

Versioning


No version available

Maintainers


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Publication for BiConstruct

BiConstruct citation

library_books

Efficient parallel and out of core algorithms for constructing large bi directed de Bruijn graphs

2010
BMC Bioinformatics
PMCID: 2996408
PMID: 21078174
DOI: 10.1186/1471-2105-11-560

[…] parallelism the run time is asymptotically optimal - which means optimality within a constant. In practice coarse-grain parallelism is what we have. Here n = N (r - k + 1). We call this algorithm Par-BiConstruct.Theorem 2. Algorithm Par-BiConstruct builds a bi-directed de Bruijn graph in time O(n/p). The message complexity is O(n).The algorithm of Jackson and Aluru [] first identifies the vertices […]

BiConstruct institution(s)
Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA; Texas Advanced Computing Center, University of Texas at Austin, TX, USA; Cold Spring Harbor Laboratory, Cold Spring Habor, NY, USA
BiConstruct funding source(s)
Supported in part by grants: NSF 0326155, NSF 0829916 and NIH 1R01LM010101-01A1.

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