r2cat protocols

r2cat computational protocol

r2cat specifications


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 IN pipelines

PMCID: 5629057
PMID: 28983000
DOI: 10.1128/genomeA.01073-17

[…] the sequence data were assembled using the a5-miseq assembler (17), and the genome sequence was annotated via the ncbi prokaryotic genome annotation pipeline (18). the contigs were reordered with r2cat (19). the genome statistics are shown in table 1., antibiotic resistance genes were identified using arg-annot (20). all isolates had at least one extended-spectrum β-lactamase (esbl) […]

PMCID: 5059922
PMID: 27729005
DOI: 10.1186/s12864-016-3140-1

[…] mannheim, germany) with default settings. in our approach, we used a 2 x 300 bp paired end sequencing run. for quality-control and filtering, a pipeline including trimmomatic (bolger et al. [45]), r2cat [46] and contig-length vs. read-count analysis [47, 48] was implemented. the resulting data set was manually inspected and improved., based on contig length vs. read count analysis [47–49] […]

PMCID: 5059922
PMID: 27729005
DOI: 10.1186/s12864-016-3140-1

[…] species of frankia in the metagenome dataset, a reference assembly was applied. for reference assembly, metagenomic contigs were mapped onto the reference genome frankia sp. dg1 [15] by means of r2cat [46]. mapped contigs and their corresponding reads were extracted and de novo assembled using the gs assembler (version 2.8; roche) with default settings. furthermore, automatic gene prediction […]

PMCID: 4447923
PMID: 26021938
DOI: 10.1128/genomeA.00572-15

[…] software (release 2.8), resulting in 16 scaffolds and 22 scaffolded contigs. the scaffolds were ordered by synteny analysis with the chromosome of corynebacterium vitaeruminis (9) using the r2cat tool (10). gaps were bridged by adding 9,325 mate pair reads to the assembly. these reads were derived from dna sequencing with the miseq reagent kit v3 (600 cycles) of a 7-kb mate pair library […]

PMCID: 4246156
PMID: 25428964
DOI: 10.1128/genomeA.01180-14

[…] to the read qualities. we followed the a5-miseq pipeline (9) for read trimming, correction, contig assembly, and scaffolding. we performed a further step of misassembling correction using the r2cat tool (10) and then reordered the scaffolds with mauve (11) using cbuk_q154 (12) as the reference genome, having genotype 8 phylogenetically close to mst51., sequencing resulted in 3 scaffolds […]

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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