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Currently Supported Genomes

These are the currently supported genomes:

For analyses made with the formerly distributed reference archives, see the Legacy reference guide for installation and usage.

  • GRCh38.p12 [GRCh38]
    GRCh38.p12 [GRCh38] (Genome Reference Consortium Human Reference 38), INSDC Assembly GCA_000001405.27, Dec 2013. Released July 2014. Last updated January 2018.
    This genome was downloaded from ENSEMBL database version 93.38.

  • GRCh37.p13 [GRCh37]
    GRCh37.p13 [GRCh37] (Genome Reference Consortium Human Reference 37), INSDC Assembly GCA_000001405.14, Feb 2009. Released April 2011. Last updated September 2013.
    This genome was downloaded from ENSEMBL database version 93.37.

GRCh37 contains corrected transcription-strand labels and is recommended for new analyses. GRCh37_Legacy retains the historical labels for reproducibility.

  • GRCm39 [mm39]
    GRCm39 [mm39] (Genome Reference Consortium Mouse Reference 39), INSDC Assembly GCA_000001635.9, Jun 2020. Last updated August 2020.
    This genome was downloaded from ENSEMBL database version 103.

mm39 uses corrected transcription-strand data for new analyses. The previously distributed reference is available as mm39_Legacy for reproducing historical results; existing local mm39 installations must be reinstalled after upgrading. See the mm39 reference record.

  • GRCm38.p6 [mm10]
    GRCm38.p6 [mm10] (Genome Reference Consortium Mouse Reference 38), INDSDC Assembly GCA_000001635.8, Jan 2012. Released July 2012. Last updated March 2018.
    This genome was downloaded from ENSEMBL database release 94 (previously documented as "93.38"; see reference_data/mm10/README.md). Use mm10 for corrected transcription-strand annotation; use mm10_Legacy only to reproduce historical results.

  • GRCm37 [mm9]
    GRCm37 [mm9] (Release 67, NCBIM37), INDSDC Assembly GCA_000001635.18. Released Jan 2011. Last updated March 2012.
    This genome was downloaded from ENSEMBL database version release 67. Use mm9 for corrected transcription-strand annotation; use mm9_Legacy only to reproduce historical results.

  • rn6 [Rnor_6.0]
    Rnor_6.0, INSDC Assembly GCA_000001895.4, Jul 2014. Released Jun 2015. Last updated Jan 2017.
    This genome was downloaded from ENSEMBL database version 96.6.

  • yeast [Saccharomyces cerevisiae S288C; assembly R64-2-1]
    yeast [Saccharomyces cerevisiae S288C; assembly R64-2-1]. Released Nov 2014.

  • EBV [Epstein-Barr Virus]
    ebv [EBV] NC_007605.1, Nov 2005. Last updated Aug 2018. This genome was downloaded from the NCBI database: https://www.ncbi.nlm.nih.gov/nuccore/82503188/.

  • dog [CanFam3.1]
    dog [CanFam3.1] GCA_000002285.2, Sep 2011. Last updated Jun 2019. This genome was downloaded from ENSEMBL database version 100.

  • c_elegans [WBcel235]
    WBcel235 [c_elegans] GCA_000002985.3, Oct 2014. Last updated Jan 2019. This genome was downloaded from ENSEMBL database version 100.