Phre/Phrap & Reference Sequence

Martin Brandon mbrandon at mindspring.com
Thu Jan 10 08:20:03 EST 2002

I've been struggling with phrap on and off for a few months now.  Our
lab sequences human mitochondrial DNA (16.5 KB) and I would like to
use a reference sequence (Cambridge mitochondrial sequence) as a
scaffolding for the assemblies.  I have successfully made a fake phd
read of the reference sequence, but I only want it to anchor the reads
in the correct location and not be used in the generation of the
consensus sequence.  Is this possible with phrap?  I have some time
invested in learning the setup of this software, but would be
interested if anyone has found a better alternative.

The goal is to try and automate the process of extracting
mitochondrial DNA differences from the raw data.  Right now, my
assemblies are always quite a bit off (usually one or two reads that
stick out significantly).  Are there any special considerations for
working with a circular genome?


Martin Brandon
mbrandon at mindspring.com
Emory University - CMM


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