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Currently Supported Genomes

This page lists all reference genomes currently supported by SigProfilerMatrixGenerator.

Summary Table

Organism Genome Build Alias Source
Human GRCh38.p12 GRCh38 ENSEMBL v93.38
Human GRCh37.p13 GRCh37 ENSEMBL v93.37
Mouse GRCm39 mm39 ENSEMBL v103
Mouse GRCm38.p6 mm10 ENSEMBL v93.38
Mouse GRCm37 mm9 ENSEMBL v67
Rat Rnor_6.0 rn6 ENSEMBL v96.6
Yeast S288C R64-2-1 yeast -
Epstein-Barr Virus NC_007605.1 ebv NCBI
Dog CanFam3.1 dog ENSEMBL v100
C. elegans WBcel235 c_elegans ENSEMBL v100

Detailed Genome Information

Human Genomes

GRCh38 (GRCh38.p12)

  • Full Name: Genome Reference Consortium Human Reference 38
  • INSDC Assembly: GCA_000001405.27
  • Release Date: December 2013 (Released July 2014, Last updated January 2018)
  • Source: ENSEMBL database version 93.38
genInstall.install('GRCh38')

GRCh37 (GRCh37.p13)

  • Full Name: Genome Reference Consortium Human Reference 37
  • INSDC Assembly: GCA_000001405.14
  • Release Date: February 2009 (Released April 2011, Last updated September 2013)
  • Source: ENSEMBL database version 93.37
genInstall.install('GRCh37')

Mouse Genomes

mm39 (GRCm39)

  • Full Name: Genome Reference Consortium Mouse Reference 39
  • INSDC Assembly: GCA_000001635.9
  • Release Date: June 2020 (Last updated August 2020)
  • Source: ENSEMBL database version 103
genInstall.install('mm39')

mm10 (GRCm38.p6)

  • Full Name: Genome Reference Consortium Mouse Reference 38
  • INSDC Assembly: GCA_000001635.8
  • Release Date: January 2012 (Released July 2012, Last updated March 2018)
  • Source: ENSEMBL database version 93.38
genInstall.install('mm10')

mm9 (GRCm37)

  • Full Name: Release 67, NCBIM37
  • INSDC Assembly: GCA_000001635.18
  • Release Date: January 2011 (Last updated March 2012)
  • Source: ENSEMBL database version release 67
genInstall.install('mm9')

Rat Genome

rn6 (Rnor_6.0)

  • INSDC Assembly: GCA_000001895.4
  • Release Date: July 2014 (Released June 2015, Last updated January 2017)
  • Source: ENSEMBL database version 96.6
genInstall.install('rn6')

Other Organisms

Yeast (Saccharomyces cerevisiae S288C)

  • Assembly: R64-2-1
  • Release Date: November 2014
genInstall.install('yeast')

Epstein-Barr Virus (EBV)

  • Accession: NC_007605.1
  • Release Date: November 2005 (Last updated August 2018)
  • Source: NCBI database
genInstall.install('ebv')

Dog (CanFam3.1)

  • INSDC Assembly: GCA_000002285.2
  • Release Date: September 2011 (Last updated June 2019)
  • Source: ENSEMBL database version 100
genInstall.install('dog')

C. elegans (WBcel235)

  • INSDC Assembly: GCA_000002985.3
  • Release Date: October 2014 (Last updated January 2019)
  • Source: ENSEMBL database version 100
genInstall.install('c_elegans')

Installation Example

To install a reference genome:

from SigProfilerMatrixGenerator import install as genInstall
genInstall.install('GRCh37')  # Replace with your desired genome

Note: Each genome requires approximately 3 GB of storage space. The installation process may take some time due to the large file sizes.