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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: synteny plots and comparative assembly
r2cat citations
(19)Reclassification of Paenibacillus riograndensis as a Genomovar of Paenibacillus sonchi: Genome Based Metrics Improve Bacterial Taxonomic Classification
[…] 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 […]
Non autotrophic methanogens dominate in anaerobic digesters
[…] 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. […]
Proteogenomics produces comprehensive and highly accurate protein coding gene annotation in a complete genome assembly of Malassezia sympodialis
[…] 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. […]
An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH
[…] 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. […]
Comparative Genomics and Metabolic Analysis Reveals Peculiar Characteristics of Rhodococcus opacus Strain M213 Particularly for Naphthalene Degradation
[…] 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. […]
Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine
[…] 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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