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.