GenomeScope: Fast Reference-free Genome Profiling from Short Reads

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2017 Apr 4

PMID 28369201

Citations 837

Authors

Gregory W Vurture

Fritz J Sedlazeck

Maria Nattestad

Charles J Underwood

Han Fang

James Gurtowski

Michael C Schatz

Affiliations

Soon will be listed here.

Abstract

Summary: GenomeScope is an open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate and repeat content from unprocessed short reads. These features are essential for studying genome evolution, and help to choose parameters for downstream analysis. We demonstrate its accuracy on 324 simulated and 16 real datasets with a wide range in genome sizes, heterozygosity levels and error rates.

Availability And Implementation: http://genomescope.org , https://github.com/schatzlab/genomescope.git .

Contact: mschatz@jhu.edu.

Supplementary Information: Supplementary data are available at Bioinformatics online.

Citing Articles

Chromosome-level genome assembly of a critically endangered species Leuciscus chuanchicus.

Wang Q, Zhou Q, Liu H, Li J, Jiang Y Sci Data. 2025; 12(1):441.

PMID: 40089515 DOI: 10.1038/s41597-025-04787-2.

A chromosomal-level genome assembly of Begonia fimbristipula (Begoniaceae).

Xiao T, Wang Z, Yan H Sci Data. 2025; 12(1):429.

PMID: 40074751 PMC: 11904028. DOI: 10.1038/s41597-025-04768-5.

Chromosome-level genome assembly of the clam, Xishi tongue Coelomactra antiquata.

Shen Y, Wang Y, Kong L Sci Data. 2025; 12(1):422.

PMID: 40069159 PMC: 11897284. DOI: 10.1038/s41597-025-04734-1.

High-resolution genome assembly and population genetic study of the endangered maple (Sapindaceae): implications for conservation strategies.

Li X, Jiang L, Deng H, Yu Q, Ju W, Chen X Hortic Res. 2025; 12(4):uhae357.

PMID: 40066161 PMC: 11891484. DOI: 10.1093/hr/uhae357.

Chromosome-level genome assembly and annotation of pawak croaker (Pennahia pawak).

Jiang L, Zheng P, Zheng J, Liu Y, Song W, Chen S Sci Data. 2025; 12(1):412.

PMID: 40064941 PMC: 11894176. DOI: 10.1038/s41597-025-04745-y.

References

Kelley D, Schatz M, Salzberg S . Quake: quality-aware detection and correction of sequencing errors. Genome Biol. 2010; 11(11):R116. PMC: 3156955. DOI: 10.1186/gb-2010-11-11-r116. View

Li X, Waterman M . Estimating the repeat structure and length of DNA sequences using L-tuples. Genome Res. 2003; 13(8):1916-22. PMC: 403783. DOI: 10.1101/gr.1251803. View

Goodwin S, McPherson J, McCombie W . Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016; 17(6):333-51. PMC: 10373632. DOI: 10.1038/nrg.2016.49. View

Simpson J . Exploring genome characteristics and sequence quality without a reference. Bioinformatics. 2014; 30(9):1228-35. PMC: 3998141. DOI: 10.1093/bioinformatics/btu023. View

Phillippy A, Schatz M, Pop M . Genome assembly forensics: finding the elusive mis-assembly. Genome Biol. 2008; 9(3):R55. PMC: 2397507. DOI: 10.1186/gb-2008-9-3-r55. View

Marcais G, Kingsford C . A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 2011; 27(6):764-70. PMC: 3051319. DOI: 10.1093/bioinformatics/btr011. View

Miller C, Hampton O, Coarfa C, Milosavljevic A . ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS One. 2011; 6(1):e16327. PMC: 3031566. DOI: 10.1371/journal.pone.0016327. View

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

Gnerre S, MacCallum I, Przybylski D, Ribeiro F, Burton J, Walker B . High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A. 2010; 108(4):1513-8. PMC: 3029755. DOI: 10.1073/pnas.1017351108. View

10.

Melsted P, Halldorsson B . KmerStream: streaming algorithms for k-mer abundance estimation. Bioinformatics. 2014; 30(24):3541-7. DOI: 10.1093/bioinformatics/btu713. View

11.

Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M . Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res. 2014; 24(8):1384-95. PMC: 4120091. DOI: 10.1101/gr.170720.113. View

12.

Chikhi R, Medvedev P . Informed and automated k-mer size selection for genome assembly. Bioinformatics. 2013; 30(1):31-7. DOI: 10.1093/bioinformatics/btt310. View

13.

Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov A . SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19(5):455-77. PMC: 3342519. DOI: 10.1089/cmb.2012.0021. View

14.

Smolka M, Rescheneder P, Schatz M, von Haeseler A, Sedlazeck F . Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol. 2015; 16:235. PMC: 4618857. DOI: 10.1186/s13059-015-0803-1. View