OcculterCut statistics

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OcculterCut specifications


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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  • person_outline Alison Testa <>

Publication for OcculterCut

OcculterCut in publications

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

[…] []. 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 […]

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 […]

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 […]

PMCID: 5737690
PMID: 29186370
DOI: 10.1093/gbe/evx242

[…] 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 ()., to search for putative genes contributing to pathogenicity, we conducted a blastp (v2.2.28+) () search with an e-value threshold of 1e–6 against the phi-base 4.0 database () […]

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

[…] signalp v4 () and output as mature proteins, lacking the signal sequence. mature secreted proteins were input into effectorp v1 () to identify putative effectors in the updated 0-1 annotation set., occultercut v1 () is a tool used to identify gc content patterns in genomes. occultercut outputs a number of useful statistics, which include the average sizes of gc-rich and poor regions, as well […]

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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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