BACCardI protocols

View BACCardI computational protocol

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BACCardI specifications

Information


Unique identifier OMICS_22186
Name BACCardI
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format ACE, FASTA
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

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Publication for BACCardI

BACCardI in pipeline

2009
PMCID: 2652115
PMID: 19283063
DOI: 10.1371/journal.pgen.1000416

[…] in pcc2fos. dna sequencing was performed using dye-terminator chemistries on abi3700 sequencers. shotgun sequences were assembled with phrap. fosmid end sequences were mapped onto the assembly using baccardi for validation and support of gap closing. sequences of all large repeat elements (rrna operons and prophages) were confirmed by primer walking of fosmid clones., the nucleotide sequence […]


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BACCardI in publications

 (5)
PMCID: 3599525
PMID: 23351674
DOI: 10.1186/1475-2875-12-36

[…] pidgin, frederique ottou in french, princess khadizah in fulfulde, sine in english and french, xmaleya in english and french, and a combination message in french and english from xmaleya, sine, pit baccardi, and afo akom) were on air at least once daily from 1 april to 1 july, 2012.b, in addition to donating media distribution of the psas, mtn made an in-kind contribution of net-use reminders […]

PMCID: 3103447
PMID: 21486487
DOI: 10.1186/1471-2105-12-95

[…] tools such as bambus [] allow the incorporation of mate-pair data into virtually any assembly []. furthermore, mate-pairs are frequently used for the purpose of assembly validation in tools such as baccardi [], consed [], and hawkeye []., most of the research on the use of mate-pair information in genome projects has focused primarily on the use of this information to achieve long-range […]

PMCID: 2830990
PMID: 20137072
DOI: 10.1186/1471-2164-11-91

[…] mwg operon., to verify the assembly of the c. aurimucosum atcc 700975 genome sequence, the paired-end sequence information obtained from fosmid clones was used to generate a genomic map with the baccardi program []. automated annotation of the c. aurimucosum genome sequence was carried out with the bacterial genome annotation platform gendb [] as described earlier [], followed by manual […]

PMCID: 2652115
PMID: 19283063
DOI: 10.1371/journal.pgen.1000416

[…] in pcc2fos. dna sequencing was performed using dye-terminator chemistries on abi3700 sequencers. shotgun sequences were assembled with phrap. fosmid end sequences were mapped onto the assembly using baccardi for validation and support of gap closing. sequences of all large repeat elements (rrna operons and prophages) were confirmed by primer walking of fosmid clones., the nucleotide sequence […]

PMCID: 3055744
PMID: 19495914
DOI: 10.1007/s12575-009-9004-1

[…] for this purpose. examples of manual finishing software are components of the aforementioned consed: sequence finishing tool [] and redit: shotgun assembly finishing aid [], also others include baccardi: validate and assist in finishing [] and dnptrapper: analysis of complex regions and finishing tool []. each of these software programs aim to make the editing process as user friendly […]


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BACCardI institution(s)
Universität Bielefeld, Center for Biotechnology (CeBiTec), Bielefeld, Germany; Universität Bielefeld, Lehrstuhl für Genetik, Fakultät für Biologie, Bielefeld, Germany; Max-Planck-Institut für Biochemie, Abt. Membranbiochemie, Martinsried, Germany; Max-Planck-Institut für Entwicklungsbiologie, Tübingen, Germany; Universität Bielefeld, Technische Fakultät, Bielefeld, Germany

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