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OcculterCut specifications

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Unique identifier OMICS_14690
Name OcculterCut
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data The software describes genome segmentation and segment classification steps and outputs a number of files containing the results of these steps.
Operating system Unix/Linux
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Alison Testa

Publication for OcculterCut

OcculterCut citations

 (7)
library_books

Comparative genomics of the wheat fungal pathogen Pyrenophora tritici repentis reveals chromosomal variations and genome plasticity

2018
BMC Genomics
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] nucBed []. Isolate average read coverage was calculated over a window size of 1000 bp using SAMTools bedcov v0.1.19 [] and BEDTools genomecov v2.17.0 [].The AT richness of genomes was assessed using Occultercut –v1.1 [].Isolated gene predictions, transcripts and reference GFF3 file comparisons were made with BEDTools version 2.17.0 intersect [, ].Core orthologous gene groups from OrthoFinder anal […]

library_books

Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host–Pathogen Genetic Interactions

2018
Front Genet
PMCID: 5915480
PMID: 29720997
DOI: 10.3389/fgene.2018.00130

[…] Mbp. Moreover, the mean length of the long-read PTT genome assemblies is 21% longer than PTM and the length of GC-equilibrated sequence representing coding DNA and recent TE insertions, estimated by OcculterCut (), is 9% longer in PTT than PTM (Table , with whole genome GC distribution graphically shown in Figure ).Long DNA read genome assemblies enable a more complete catalog of the repetitive D […]

library_books

Reference Quality Genome Assemblies of Three Parastagonospora nodorum Isolates Differing in Virulence on Wheat

2017
PMCID: 5919747
PMID: 29233913
DOI: 10.1534/g3.117.300462

[…] genomic compartments exist, consisting of marked differences in GC content (). The genome architecture of P. nodorum isolates Sn4, Sn2000, and Sn79-1087 were examined with regard to GC content using OcculterCut with default settings ().Synteny analysis was conducted in SyMAP v4.2 (). Sn4 nuclear contigs were sorted from largest to smallest and used as a reference for alignment. Nuclear contigs of […]

library_books

Comparative Genomics of Pathogenic and Nonpathogenic Beetle Vectored Fungi in the Genus Geosmithia

2017
Genome Biol Evol
PMCID: 5737690
PMID: 29186370
DOI: 10.1093/gbe/evx242

[…] s and tend to favor the conversion of cytosines to thymines resulting in AT-rich regions (). Therefore, we also examined whether Geosmithia species have undergone repeat-induced point mutations using OcculterCut v1.1 (). […]

library_books

Reference Assembly and Annotation of the Pyrenophora teres f. teres Isolate 0 1

2017
PMCID: 5765338
PMID: 29167271
DOI: 10.1534/g3.117.300196

[…] P may be a contributing factor in the development of AT-rich genome regions. Evolution rates of genes in close proximity to AT-rich regions could be increased through the aid of RIP (; ). The program OcculterCut v1 () was used to examine the overall GC content of the genome. The output of this analysis resulted in two distinct genome categories: one with high GC content (41–100%) and the other wit […]

library_books

Evaluation of single cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis

2017
Sci Rep
PMCID: 5591225
PMID: 28887541
DOI: 10.1038/s41598-017-11466-9

[…] mean variance and trained according to a previous study.Third, we confirmed that the GC content distribution did not present two peaks after removing the contaminant scaffolds, and, using the program OcculterCut, that the GC content was similar to the reference genome. Finally, we searched for the presence of prokaryotic 16S rDNA sequences by performing a BLASTn of the 16S rDNA gene sequence on ou […]


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OcculterCut institution(s)
Department of Environment & Agriculture, Centre for Crop and Disease Management, Curtin University, Perth, Australia; Curtin Institute for Computation, Curtin University, Perth, Australia
OcculterCut funding source(s)
Supported by the Australian Federal Government and by the Grains Research & Development Corporation (GRS10564).

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