Entering edit mode
10.3 years ago
rob234king
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610
I've established through mapping paired end reads to a partially completed reference that a 4-5kb sequence at the end of the contig exists on the 3' end of a chromosome repeated twice but it should be repeated ten times (because coverage compared to rest of sequence is many times greater) however this repeat sequence has not been assembled for obvious reasons given its a recurring sequence. I was wondering if there was software which extends the 3' end sequence using reads up as it goes, or a assembler that could deal with this better than SOAP2 or some other way to resolve this sequence without resequencing.
not sure if this will help but GRC wrote about their strategy to sequence centromeres in humans here