I want to align the sugarcane RNA-seq reads against reference genome of sugarcane but the complete genome assembly is not available to date. Please guide which reference sequence/assembly can be used for this purpose. Thanks!
Looks like you best bet may be to get the data from Sugarcane Genome Hub.
Ensembl has Saccharum spontaneum which is likely not what you want. NCBI also seems to have the same species.
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