GenomeScope2¶

Description¶

GenomeScope 2.0 applies classical insights from combinatorial theory to establish a detailed mathematical model of how k-mer frequencies will be distributed in heterozygous and polyploid genomes.

Environment Modules¶

Run module spider genomescope2 to find out what environment modules are available for this application.

Environment Variables¶

HPC_GENOMESCOPE2_DIR - installation directory
HPC_GENOMESCOPE2_BIN - executable directory

Citation¶

If you publish research that uses GenomeScope2 you have to cite it as follows:

Ranallo-Benavidez, T. R., Jaron, K. S., & Schatz, M. C. (2020). GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nature Communications, 11, 1432. https://doi.org/10.1038/s41467-020-14998-3
Vurture, G. W., Sedlazeck, F. J., Nattestad, M., Underwood, C. J., Fang, H., Gurtowski, J., & Schatz, M. C. (2017). GenomeScope: Fast reference-free genome profiling from short reads. Bioinformatics, 33(14), 2202–2204. https://doi.org/10.1093/bioinformatics/btx153

Categories¶

phylogenetics