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GenomeScope specifications

Information


Unique identifier OMICS_12887
Name GenomeScope
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Michael Schatz

Information


Unique identifier OMICS_12887
Name GenomeScope
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Javascript, PHP, R
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Michael Schatz

Publication for GenomeScope

GenomeScope citations

 (21)
library_books

A draft genome sequence for the Ixodes scapularis cell line, ISE6

2018
F1000Res
PMCID: 5883391
PMID: 29707202
DOI: 10.5256/f1000research.14813.r31696

[…] rsion 1.2.1 and bedtools ( ; ) version 2.26. K-mers were counted using Jellyfish ( ) version 2.2.6 for several values of K: 11, 15, 21, 41, 51, and 61. Each computed K-mer histogram was analyzed with GenomeScope ( ). Single-copy gene analysis used BUSCO ( ) version 3.0.2 with Arthropoda OrthoDB version 9. Alignments between the tick and cell line assemblies were computed on contigs from each assem […]

library_books

A Near Complete Haplotype Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity

2018
MBio
PMCID: 5821087
PMID: 29463659
DOI: 10.1128/mBio.02275-17

[…] id genomes ().Previous unphased P. striiformis f. sp. tritici genome assemblies ranged in size from 53 to 115 Mb (, , , ). In an attempt to reconcile the differences in reported genome sizes, we used GenomeScope to estimate the haploid genome size, using k-mer frequencies (30-mers) in two Illumina short-read data sets of Pst-104E (). Based on this analysis, we estimated a haploid genome size of 68 […]

library_books

De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust

2018
MBio
PMCID: 5821079
PMID: 29463655
DOI: 10.1128/mBio.01650-17

[…] SRR4063847) (), Puccinia striiformis f. sp. tritici (SRR058505 and SRR058506) (), Puccinia triticina (SRR027504 and SRR027505), and Melampsora lini (). The resulting histograms were used as input for GenomeScope ().To identify structural variations (SVs), haplotigs were aligned to primary contigs with MUMmer (v3.23) with the following parameters: nucmer -maxmatch -l 100 -c 500 (). SVs were detecte […]

library_books

Whole genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)

2018
Sci Rep
PMCID: 5784092
PMID: 29367590
DOI: 10.1038/s41598-018-19430-x

[…] ith the teleost specific whole genome duplication event (TS-WGD). And like many marine organisms, the angelfish has a large effective population size resulting in a high heterozygosity rate of 1.36% (GenomeScope). Both of these features present significant challenges to whole genome assemblies. The success of the Chicago/HiRise long-range scaffolding method in overcoming these challenges for the a […]

library_books

Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly

2018
BMC Genomics
PMCID: 5773036
PMID: 29343235
DOI: 10.1186/s12864-018-4434-2

[…] Quake [] with the following parameters: minimum length of reads ≥ 70 bp and minimum quality ≥ 20. The filtered reads were used to identify heterozygosity using JELLYFISH [] with –m 19 option and with GenomeScope []. A de novo genome assembly was developed using PLATANUS (version 1.2.4) [] with default parameters (PLAT_d). The previously published ALLPATHS-LG assembly (AP) and PLAT_d were merged it […]

library_books

Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly

2018
GigaScience
PMCID: 5848817
PMID: 29342277
DOI: 10.1093/gigascience/gix137

[…] the “clean” Illumina reads was performed with Jellyfish v.2.2.6 (Jellyfish, RRID:SCR_005491) [], generating k-mer frequency distributions of 17-, 21-, and 25-mers. These histograms were processed by GenomeScope [], which estimated a genome size of 791 to 794 Mbp with approximately 80% of unique content and a heterozygosity level of 0.6% (). Given that we had previously excluded adapters as well a […]

Citations

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GenomeScope institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Johns Hopkins University, Baltimore, MD, USA; Stony Brook University, Stony Brook, NY, USA
GenomeScope funding source(s)
This project was supported by the National Science Foundation [DBI-¬‐1350041 and IOS-¬‐1237880] and the National Institutes of Health [R01-¬‐HG006677].

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