OptItDBA specifications

Information


Unique identifier OMICS_33262
Name OptItDBA
Alternative name Optimized Iterative De Bruijn graph Assembly
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Shell (Bash)
Computer skills Advanced
Stability Stable
Requirements
R, Python, Samtools, Bwa, SOAPdenovo-63mer
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Frederic Bushman

Publication for Optimized Iterative De Bruijn graph Assembly

OptItDBA citation

library_books

Conservation of Gene Cassettes among Diverse Viruses of the Human Gut

2012
PLoS One
PMCID: 3416800
PMID: 22900013
DOI: 10.1371/journal.pone.0042342

[…] s program, MetaIDBA, has been developed .In this paper our goal is to find patterns of genome conservation in the highly diverse collection of viruses found in the human gut , , , , . We implement an optimized iterative de Bruijn graph assembly approach, significantly increasing the length and depth of the assembled contigs compared with previous virome studies. We present results for 5.6 Gb of Il […]

OptItDBA institution(s)
Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Division of Gastroenterology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
OptItDBA funding source(s)
Supported by Human Microbiome Roadmap Demonstration Project UH2DK083981 (Wu, Bushman, Lewis, Co-PIs) and NIH Training Grant T32AI060516.

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