Bambus protocols

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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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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 in pipeline

2012
PMCID: 3366996
PMID: 22675498
DOI: 10.1371/journal.pone.0037919

[…] using minimus, resulting in a hybrid assembly for tm7a. the resulting assembly was then further combined with the homd tm7a reference genomic sequence. after assembly, scaffolds were created using bambus 2 using the available mate-pair information., we used metagene to predict genes (> = 300 bp) in the tm7 reference genome (ncbi accession nz_abbv00000000) as well as in our combined […]


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Bambus in publications

 (37)
PMCID: 5855605
PMID: 29382070
DOI: 10.3390/ijms19020383

[…] 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 […]

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

[…] regions are masked, the overlap between the two assemblies is detected using minimus []. zorro then unmasks the repetitive regions and merges overlapping contigs. lastly, zorro uses the tool bambus [] to order and orient contigs using paired-end reads. zorro was used in [] and [] to merge two assemblies., while one would expect assembly reconciliation tools to be particularly beneficial […]

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

[…] of this oleaginous red yeast was sequenced using a hybrid of roche 454 and illumina technology generating 13 × coverage. the de novo assembly was carried out using mira and scaffolded using maq and bambus. the sequencing and assembly resulted in 365 scaffolds with total genome size of 33.4 mb. the complete genome sequence of this strain was deposited in genbank and the accession number […]

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

[…] 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 […]

PMCID: 5337752
PMID: 28321234
DOI: 10.3389/fgene.2017.00023

[…] 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, […]


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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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