GenomeScope: fast reference-free genome profiling from short reads

作者：Gregory W. Vurture, Fritz J. Sedlazeck, Maria Nattestad, Charles J. Underwood, Han Fang, James Gurtowski, Michael C. Schatz · 发表于：Bioinformatics · 年份：2017 · DOI：10.1093/bioinformatics/btx153 · 被引用次数：2036 · 研究领域：Genome Rearrangement Algorithms、Genomics and Phylogenetic Studies、Algorithms and Data Compression

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.