GenomeScope: Fast reference-free genome profiling from short reads

By Gregory W. Vurture, Fritz J. Sedlazeck, Maria Nattestad, Charles J. Underwood, Han Fang, James Gurtowski, Michael C. Schatz. bioRxiv, 2016

1,665 citations recorded by the source corpus.

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.

Subfields: Artificial Intelligence, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ea398413f2827444c455325dfe1c3846cef0c543

Citations in the corpus

• HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads (2020, neutral): “S1; Vurture et al. 2017).”