[Bioperl-l] Simulate fragment and read-pair reads from sample sequence

Albert Vilella avilella at gmail.com
Mon Feb 15 08:45:10 EST 2010


This may have been asked before but I couldn't find any similar
question by searching the archives.
I want to simulate substr's from a sequence of a given (read) length.

If I have a starting sequence of 10,000bp, the way I understand it is
that a standard Solexa (or 454) library
preparation will give me random $read_length=75 (or 450) reads along
the 10k sequence.
So I want to do a random substr on the sequence itself.

But if I am simulating read-pairs of a 10,000bp sequence, given a
defined $insert_size length, how would I
do the random substr pairs?



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