Supported Genomes¶
This section lists all reference genomes currently supported by SigProfilerSimulator. Reference genomes must be installed using SigProfilerMatrixGenerator before running simulations.
Available Reference Genomes¶
| Genome ID | Assembly | Species | Source | Last updated |
|---|---|---|---|---|
GRCh38 |
GRCh38.p12 (GCA_000001405.27) | Homo sapiens | ENSEMBL v93.38 | January 2018 |
GRCh37 |
GRCh37.p13 (GCA_000001405.14) | Homo sapiens | ENSEMBL v93.37 | September 2013 |
mm10 |
GRCm38.p6 (GCA_000001635.8) | Mus musculus | ENSEMBL v93.38 | March 2018 |
mm9 |
GRCm37 (GCA_000001635.18) | Mus musculus | ENSEMBL release 67 | March 2012 |
rn6 |
Rnor_6.0 (GCA_000001895.4) | Rattus norvegicus | ENSEMBL v96.6 | January 2017 |
yeast |
R64-2-1 | Saccharomyces cerevisiae S288C | NCBI | November 2014 |
Installation¶
Install a reference genome from the command line:
$ SigProfilerMatrixGenerator install GRCh37
Or from a Python terminal:
$ python
>>> from SigProfilerMatrixGenerator import install as genInstall
>>> genInstall.install('GRCh37', rsync=False, bash=True)
Multiple genomes can be installed independently. For full installation details, refer to the Installation section.