DOE CODE   /    Search Results   /    diBELLA 2D: Parallel String Graph Construction and Transitive Reduction for De Novo Assembly (diBELLA 2D) v1.0

diBELLA 2D: Parallel String Graph Construction and Transitive Reduction for De Novo Assembly (diBELLA 2D) v1.0

RESOURCE

Publicly Accessible Repository
https://github.com/PASSIONLab/diBELLA.2D
https://doi.org/10.11578/dc.20210311.2

SAVE / SHARE



LBNL Badge

Abstract

In this work we present a 2D distributed memory algorithm for overlap detection and introduce a novel design and implementation for layout simplification where we perform a transitive reduction from overlap graph to string graph in the context of de novo genome assembly.
Developers:
Buluc, Aydin [1] ;  Guidi, Giulia [1]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Release Date:
2021-02-09
Project Type:
Open Source, Publicly Available Repository
Software Type:
Scientific
Licenses:
BSD 3-clause "New" or "Revised" License
Sponsoring Org.:
Code ID:
52577
Site Accession Number:
2021-012
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Country of Origin:
United States

RESOURCE

Publicly Accessible Repository
https://github.com/PASSIONLab/diBELLA.2D
https://doi.org/10.11578/dc.20210311.2

SAVE / SHARE



LBNL Badge

Citation Formats

Buluc, Aydin, and Guidi, Giulia. diBELLA 2D: Parallel String Graph Construction and Transitive Reduction for De Novo Assembly (diBELLA 2D) v1.0. Computer Software. https://github.com/PASSIONLab/diBELLA.2D. Oak Ridge National Laboratory, USDOE. 09 Feb. 2021. Web. doi:10.11578/dc.20210311.2.
Buluc, Aydin, & Guidi, Giulia. (2021, February 09). diBELLA 2D: Parallel String Graph Construction and Transitive Reduction for De Novo Assembly (diBELLA 2D) v1.0. [Computer software]. https://github.com/PASSIONLab/diBELLA.2D. https://doi.org/10.11578/dc.20210311.2.
Buluc, Aydin, and Guidi, Giulia. " diBELLA 2D: Parallel String Graph Construction and Transitive Reduction for De Novo Assembly (diBELLA 2D) v1.0." Computer software. February 09, 2021. https://github.com/PASSIONLab/diBELLA.2D. https://doi.org/10.11578/dc.20210311.2.
@misc{ doecode_52577,
title = { diBELLA 2D: Parallel String Graph Construction and Transitive Reduction for De Novo Assembly (diBELLA 2D) v1.0},
author = {Buluc, Aydin and Guidi, Giulia},
abstractNote = {In this work we present a 2D distributed memory algorithm for overlap detection and introduce a novel design and implementation for layout simplification where we perform a transitive reduction from overlap graph to string graph in the context of de novo genome assembly.},
doi = {10.11578/dc.20210311.2},
url = {https://doi.org/10.11578/dc.20210311.2},
howpublished = {[Computer Software] \url{https://doi.org/10.11578/dc.20210311.2}},
year = {2021},
month = {feb}
}