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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

Versioning


No version available

Publication for related reference contig arrangement tool

r2cat citations

 (19)
library_books

Reclassification of Paenibacillus riograndensis as a Genomovar of Paenibacillus sonchi: Genome Based Metrics Improve Bacterial Taxonomic Classification

2017
Front Microbiol
PMCID: 5632714
PMID: 29046663
DOI: 10.3389/fmicb.2017.01849

[…] GAAP), which combines Hidden Markov Model (HMM)-based gene prediction methods with homology-based methods ().Genome assembly quality was assessed with Quast version 2.3 () and Checkm version 0.9.6 ().R2cat () is a contig arrangement tool used to order a set of contigs with respect to a single reference genome, in which mapping of the contigs onto the reference is based on a q-gram filter. The resu […]

library_books

Non autotrophic methanogens dominate in anaerobic digesters

2017
Sci Rep
PMCID: 5431450
PMID: 28473726
DOI: 10.1038/s41598-017-01752-x

[…] is (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. […]

library_books

Proteogenomics produces comprehensive and highly accurate protein coding gene annotation in a complete genome assembly of Malassezia sympodialis

2017
Nucleic Acids Res
PMCID: 5389616
PMID: 28100699
DOI: 10.1093/nar/gkx006

[…] m 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 from this study. […]

library_books

An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH

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

[…] s. 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. […]

call_split

Comparative Genomics and Metabolic Analysis Reveals Peculiar Characteristics of Rhodococcus opacus Strain M213 Particularly for Naphthalene Degradation

2016
PLoS One
PMCID: 4988695
PMID: 27532207
DOI: 10.1371/journal.pone.0161032
call_split See protocol

[…] Additionally, the draft genome sequence of strain M213 was reordered using the complete genome sequence of the type strains R. opacus B4 and R. jostii RHA1 as the reference genomes. For this purpose, r2cat (related reference contig arrangement tool) was used [], which facilitated the comparative genomics of strain M213, especially at the syntenic level. […]

library_books

Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine

2016
PMCID: 4932478
PMID: 27110816
DOI: 10.3390/pharmaceutics8020015

[…] ation. Tools such as Ensembl, GARSA, and SABIA have also been widely used for improving genome annotation [,,].Contigs orientation and visualization. Tools such as CONTIGuator, Projector2, OSLay, and r2cat could are to visualize and arrange contigs and estimate gaps compared with a reference genome [,,,].Extending contigs and filling gaps. Tools such as GAA program and Reconciliator, integrate sev […]

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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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