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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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Documentation


Maintainer


  • person_outline Michael Schatz <>

Publication for GenomeScope

GenomeScope in pipeline

2017
PMCID: 5905499
PMID: 29253216
DOI: 10.1093/gigascience/gix125

[…] using a perl script (trimadaptor.pl), and sequences that did not contain the circularization adaptor were discarded. by using the filtered short reads, jellyfish2 (jellyfish, rrid:scr_005491) [] and genomescope [] were applied to obtain estimates of the h. impetiginosus genome size, repeat fraction, and heterozygosity prior to the assembly. allpaths-lg (allpaths-lg, rrid:scr_010742) [] was used […]


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GenomeScope in publications

 (17)
PMCID: 5883391
PMID: 29707202
DOI: 10.5256/f1000research.14813.r31696

[…] 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 […]

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

[…] 0.03 mb., 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 […]

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

[…] the rust species melampsora larici-populina, melampsora lini, p. striiformis f. sp. tritici, and puccinia triticina using a k-mer profile approach based on available illumina reads with the software genomescope (). in this analysis, homozygous genomes display a simple poisson distribution in the k-mer profile plots, whereas heterozygous genomes give a bimodal profile. the k-mer profiles […]

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

[…] angelfish is based on cytogenetic work, from which a haploid genome size of 700 mb was calculated. we obtained a short read kmer-based genome length estimate of 606.8 mb using preqc. we also used genomescope to estimate genome size of 565.2 mb and heterozygosity rate of 1.36% (fig. s1). these numbers suggest that our assembly is complete, has no missing sequences, and that these results […]

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

[…] [] 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 […]


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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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