r2cat pipeline

r2cat specifications

Information


Unique identifier OMICS_06935
Name r2cat
Alternative name related reference contig arrangement tool
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for related reference contig arrangement tool

r2cat citations

 (3)
2017
PMCID: 5624749

[…] yielded 757,408 reads, accounting for 227.22 mb of total sequence information. assembly of all sequence reads applying the gs de novo assembler software (version 2.8) and reference mapping using r2cat (8) resulted in the draft sequences of the chromosome and the f plasmid of e. coli krx, comprising 68 scaffolds and 110 contigs. annotation of the chromosome was accomplished within the gendb […]

2013
PMCID: 3589621

[…] to ensure that all the contigs built from the oligo-captured dna were wvulc sequences, we aligned and ordered them to the previously sequenced wvulc genome using mauve (darling et al. 2010) and r2cat (husemann and stoye 2010). overall, 95.7 % of the bases in contigs built from oligo-captured dna were wvulc, which represents 76 % of the 1.66 mb concatenated reference genome. 61 contigs […]

2010
PMCID: 3022926

[…] was present in three tandem copies in the assembled chromosome (data not shown). the remaining gaps were closed by a pcr strategy that was supported by the related reference contig arrangement tool r2cat [13], using the corynebacterium diphtheriae nctc 13129 genome sequence as a reference [14]. the final assembly of the dna sequences yielded a circular chromosome with a size of 2,337,913 bp […]

r2cat institution(s)
Genome Informatics, Faculty of Technology, Bielefeld University, Germany; International NRW Graduate School in Bioinformatics and Genome Research, Bielefeld, Germany

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