You are here:

Reference Genomes

u Human, UCSC hg19—This reference genome is PAR-masked. This means that the pseudoautosomal regions of the Y chromosome are masked to Ns to avoid mismapping of reads.
u Human, NCBI GRCh38Decoy—This reference genome is PAR-masked.
u Chicken, Ensembl Galgal4
u Cow, Ensembl UMD3.1
u Dog, Ensembl CanFam3.1
u Maize, Ensembl AGPv3
u Mouse, UCSC mm9
u Pig, Ensembl Sscrofa10.2
u Rat, UCSC rn4
u Rice, Ensembl IRGSP-1.0
u Sheep, Ensembl Oar_v3.1
u Soybean, Ensembl Gm01
u Custom Genome—Select a FASTA file (*.fa or *.fasta) as the custom genome for the analysis.


When using a custom manifest file, specify a reference genome in the [Header] section or Build ID column of the [Probes] section. The build ID, such as hg19 or GrCh38Decoy, is case-sensitive and is used to match a built-in genome. However, if you are using a custom manifest file with a custom genome, the Build ID column of the [Probes] section is not used to find the reference genome.

For Research Use Only. Not for use in diagnostic procedures. 

©2018 Illumina, Inc. All rights reserved.