diBELLA 2D: Parallel String Graph Construction and Transitive Reduction for De Novo Assembly (diBELLA 2D) v1.0
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
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.
- Short Name / Acronym:
- diBELLA: Distributed Long Read to Long Read Assembler
- Project Type:
- Open Source, Publicly Available Repository
- Site Accession Number:
- 2021-012
- Software Type:
- Scientific
- License(s):
- BSD 3-clause "New" or "Revised" License
- Research Organization:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Organization:
- Oak Ridge National Laboratory; USDOEPrimary Award/Contract Number:AC05-00OR22725; AC02-05CH11231
- DOE Contract Number:
- AC05-00OR22725; AC02-05CH11231
- Code ID:
- 52577
- OSTI ID:
- 1770308
- Country of Origin:
- United States
Similar Records
Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly
SORA: Scalable Overlap-graph Reduction Algorithms for Genome Assembly using Apache Spark in the Cloud
NovoGraph: Human genome graph construction from multiple long-read de novo assemblies
Journal Article
·
Sat May 01 00:00:00 EDT 2021
· Proceedings - IEEE International Parallel and Distributed Processing Symposium (IPDPS)
·
OSTI ID:1770308
+3 more
SORA: Scalable Overlap-graph Reduction Algorithms for Genome Assembly using Apache Spark in the Cloud
Conference
·
Sat Dec 01 00:00:00 EST 2018
·
OSTI ID:1770308
+3 more
NovoGraph: Human genome graph construction from multiple long-read de novo assemblies
Journal Article
·
Mon Dec 10 00:00:00 EST 2018
· F1000Research
·
OSTI ID:1770308
+5 more