Phre/Phrap & Reference Sequence

Tim Cutts timc at chiark.greenend.org.uk
Mon Jan 14 04:27:00 EST 2002

In article <c411c079.0201091118.5c1d6ab at posting.google.com>,
Martin Brandon <mbrandon at mindspring.com> wrote:
>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.

Can you not fake up the quality scores of your fake read so they seem to
be extremely poor?

I used to do something similar (but sort of the other way around) for
SNP discovery using the Staden package.  We had a reference sequence
with fake perfect quality (so that the consensus sequence would always
be the reference sequence) and then performed directed assembly of
sequencing reads on that reference sequence.



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