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Reference Genomes

The following reference genomes are available for alignment:

Homo sapiens UCSC hg19 (RefSeq & Gencode gene annotations)
Homo sapiens UCSC hg38 (RefSeq & Gencode gene annotations)–The human reference genome is PAR-Masked, which means that the Y chromosome sequence has the Pseudo Autosomal Regions (PAR) masked (set to N). This setting helps prevent the mismapping of reads in the duplicate regions of sex chromosomes.
Arabidopsis thaliana Ensembl TAIR10 (Ensembl gene annotation)
Bos taurus UCSC bosTau6 (RefSeq gene annotation)
Caenorhabditis elegans UCSC ce10 (RefSeq gene annotation)
Danio rerio UCSC danRer7 (RefSeq gene annotation)
Drosophila melanogaster UCSC dm3 (RefSeq gene annotation)
Gallus gallus UCSC galGal4 (RefSeq gene annotation)
Mus musculus UCSC mm9 (RefSeq gene annotation)
Mus musculus UCSC mm10 (RefSeq gene annotation)
Oryza sativa japonica Ensembl IRGSP-1.0 (Ensembl gene annotation)
Rattus norvegicus UCSC rn5 (RefSeq gene annotation)
Saccharomyces cerevisiae Ensembl R64-1-1 (Ensembl gene annotation)
Sus scrofa UCSC susScr3 (RefSeq gene annotation)
Zea mays Ensembl AGPv3 (Ensembl gene annotation)

If you need a genome that is not listed here, use the RNA Custom Genome Builder app on BaseSpace Sequence Hub to create a custom genome.