r2cat protocols

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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 in pipelines

 (11)
2017
PMCID: 5431450
PMID: 28473726
DOI: 10.1038/s41598-017-01752-x

[…] (overbeek et al.) using the blastp program according to a method described previously. redundant functional genes were excluded from the analysis. synteny dot-plot analysis was performed using the r2cat program., nucleotide variants (polymorphisms) in the methanogen sequences were detected using basic variant detection tool in clc genomics workbench with default settings. dna reads obtained […]

2017
PMCID: 5629057
PMID: 28983000
DOI: 10.1128/genomeA.01073-17

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

2016
PMCID: 4777479
PMID: 26938641
DOI: 10.1371/journal.pone.0150550

[…] and cysa genes, insertion sequences, transposases and prophage components (6.3% of the h37rv genome replaced with gaps). contigs of 1000 bp or more were matched and sorted into h37rv order using r2cat [], aligned using mauve [] and then concatenated (with gaps inserted at junctions) into a pseudo-genome. reads were remapped against the corresponding pseudo-genome using bwa-mem [], […]

2016
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. []), r2cat [] 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 [–] […]

2016
PMCID: 5059922
PMID: 27729005
DOI: 10.1186/s12864-016-3140-1

[…] frankia sp. bmg5.23, respectively. the bioinformatics tool mauve including the progressivemauve algorithm was applied with default settings for the comparative analysis []. before applying mauve, r2cat  [] was used to adapt order and direction of contings., the sequences encoded by the open reading frames identified as putative nodh genes from the assembled dg2 metagenome (dg2nodh1, […]


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r2cat in publications

 (25)
PMCID: 5754482
PMID: 29301902
DOI: 10.1128/genomeA.01372-17

[…] sp. strain chol11 scaffolds were mapped onto the sphingobium chloroplenolium l-1 (genbank accession no. cp002798 to cp002800, bioproject no. prjna224116) reference replicons by means of r2cat (), followed by an in silico gap closure approach (). annotation of the draft replicons was performed within the gendb2.0 system () and prokka version 1.11 ()., the chol11 draft genome […]

PMCID: 5624749
PMID: 28963203
DOI: 10.1128/genomeA.00933-17

[…] 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 () 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 […]

PMCID: 5431450
PMID: 28473726
DOI: 10.1038/s41598-017-01752-x

[…] (overbeek et al.) using the blastp program according to a method described previously. redundant functional genes were excluded from the analysis. synteny dot-plot analysis was performed using the r2cat program., nucleotide variants (polymorphisms) in the methanogen sequences were detected using basic variant detection tool in clc genomics workbench with default settings. dna reads obtained […]

PMCID: 5389616
PMID: 28100699
DOI: 10.1093/nar/gkx006

[…] to avoid overestimating coverage of repeat regions. coverage profiles were computed with igvtools (). the new atcc 42132 assembly was compared to our previously published assembly () using the tool r2cat (). for centromere prediction, gc content was computed at 25 bp intervals in windows of 250 bp. gc3 content was computed in windows of 10 genes, using the final gene annotation […]

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

[…] frankia sp. bmg5.23, respectively. the bioinformatics tool mauve including the progressivemauve algorithm was applied with default settings for the comparative analysis []. before applying mauve, r2cat  [] was used to adapt order and direction of contings., the sequences encoded by the open reading frames identified as putative nodh genes from the assembled dg2 metagenome (dg2nodh1, […]


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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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