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Bambus specifications

Information


Unique identifier OMICS_01432
Name Bambus
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License Artistic License version 2.0
Computer skills Advanced
Version 2.33
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Mihai Pop

Additional information


http://amos.sourceforge.net/wiki/index.php/Bambus2 http://amos.sourceforge.net/wiki/index.php/Bambus

Publications for Bambus

Bambus citations

 (53)
library_books

Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies

2018
Int J Mol Sci
PMCID: 5855605
PMID: 29382070
DOI: 10.3390/ijms19020383

[…] nt in different proportions within the studied community.Specific assemblers have been developed for shotgun metagenomics (), such as SOAPdenovo [], Velvet [], MetaVelvet [], Meta-IBDA [], Genovo [], Bambus2 [], and Ray-Meta []. Currently, there is no unique consensus regarding the best assembly strategy, since it has been noticed that the assembler performances depend on both biological and techn […]

library_books

A comparative evaluation of genome assembly reconciliation tools

2017
Genome Biol
PMCID: 5436433
PMID: 28521789
DOI: 10.1186/s13059-017-1213-3

[…] roved over successive iterations, but the number of misassemblies also increased. For R. sphaeroides, Metassembler’s assembly did not improve after the fourth iteration. Note that NGA50 was lower for Bambus2 and SOAPdenovo. The number of misassemblies for Metassembler was about the average of the inputs. For Hg_chr14, the number of misassembly errors was low and decreased over successive iteration […]

library_books

Genome sequence of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609

2017
Genom Data
PMCID: 5440251
PMID: 28560168
DOI: 10.1016/j.gdata.2017.05.009

[…] on 2.9.43 followed by filtering of small and low coverage contigs (< 5 kb; coverage > 10 ×). Scaffolding of contigs was assisted by Illumina sequencing of 2 kb and 4 kb mate-pair libraries using Maq/Bambus . CGMCC 2.1609 assembled as 365 scaffolds with an average coverage of 13 × and a total size of 33.4 Mb. Using in-house RNA-seq and proteomic data as additional evidence, 9820 gene models were p […]

library_books

Electromembrane extraction–Recent trends and where to go

2017
PMCID: 5790682
PMID: 29404030
DOI: 10.1016/j.jpha.2017.04.002

[…] solvents in EME .In addition to pure solvents, different SLM additives have been proposed recently to enhance mass transfer , , , , . In one very interesting paper, the non-ionic macrocyclic compound bambus uril was added to nitrobenzene and used as SLM for extraction of inorganic anions . Bambus uril provided strong host-guest interactions with selected inorganic anions. Thus, with this new SLM […]

library_books

A Review of Bioinformatics Tools for Bio Prospecting from Metagenomic Sequence Data

2017
Front Genet
PMCID: 5337752
PMID: 28321234
DOI: 10.3389/fgene.2017.00023

[…] to three steps: In the first step, (meta) genome assembly is performed with a choice based on the sequencing technology used. Secondly, scaffolds are created using paired-end and mate-pair data using Bambus 2 (). Finally there is a post-assembling stage where the scaffolds are annotated and taxonomically identified. Choosing the appropriate assembler for a specific application can be difficult, an […]

library_books

Approaches for in silico finishing of microbial genome sequences

2017
Genet Mol Biol
PMCID: 5596377
PMID: 28898352
DOI: 10.1590/1678-4685-GMB-2016-0230

[…] lacing files in AFG format, and this is only produced by a few assemblers nowadays (e.g., Velvet, Ray and AMOS). SOPRA can be obtained from the website http://www.physics.rutgers.edu/~anirvans/SOPRA/.Bambus 2 (): It is part of the AMOS package () and is both a genome and metagenome scaffolding tool and an updated version of the Sanger-based program Bambus targeting NGS data (). The program require […]

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Bambus institution(s)
Department of Computer Science, University of Maryland, College Park, MD, USA; J Craig Venter Institute, Chinakville, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
Bambus funding source(s)
Supported by National Institutes of Health (R01-HG-004885); and National Science Foundation (IIS-0812111).

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