Reference Genomes
The following reference genomes are available for alignment:
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Homo sapiens UCSC hg19 (RefSeq & Gencode gene annotations) |
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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. |
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Arabidopsis thaliana Ensembl TAIR10 (Ensembl gene annotation) |
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Bos taurus UCSC bosTau6 (RefSeq gene annotation) |
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Caenorhabditis elegans UCSC ce10 (RefSeq gene annotation) |
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Danio rerio UCSC danRer7 (RefSeq gene annotation) |
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Drosophila melanogaster UCSC dm3 (RefSeq gene annotation) |
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Gallus gallus UCSC galGal4 (RefSeq gene annotation) |
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Mus musculus UCSC mm9 (RefSeq gene annotation) |
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Mus musculus UCSC mm10 (RefSeq gene annotation) |
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Oryza sativa japonica Ensembl IRGSP-1.0 (Ensembl gene annotation) |
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Rattus norvegicus UCSC rn5 (RefSeq gene annotation) |
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Saccharomyces cerevisiae Ensembl R64-1-1 (Ensembl gene annotation) |
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Sus scrofa UCSC susScr3 (RefSeq gene annotation) |
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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.