Unmasking the masked Illumina HiSeq sequences

[Rajanikanth C]

Hello world.

I want annotate the repetitive elements in an assembled genome sample. The genome assembly is platinus and the reads are of illumina HiSeq 2000 paired end platform. The assembly seems to be masked and hence on annotating i am able to identify very few annotations. Please tell me if there are any tools that i can employ to unmask the masked genome assembly.

Thanks in advance.