I have a 454 assembly from Newbler, which I know has frameshifts/unexpected stop codons in the middle of ORF's.
I would like to use a SOLiD run (which gives me 150x + coverage over the Newbler contigs) in order to correct for potential errors.
I've been using MAQ successfully to map the SOLiD reads to the Newbler contigs. However I can't see the correct - if there is one - method to extract a sequence that represents the 'overloading' of the SOLiD data. I'm using the 454 contigs as a scaffold, but I would like to extract the 'best possible' sequence over the scaffold from only the SOLiD reads.
Is there any way to do this in MAQ or in another package?
I would like to use a SOLiD run (which gives me 150x + coverage over the Newbler contigs) in order to correct for potential errors.
I've been using MAQ successfully to map the SOLiD reads to the Newbler contigs. However I can't see the correct - if there is one - method to extract a sequence that represents the 'overloading' of the SOLiD data. I'm using the 454 contigs as a scaffold, but I would like to extract the 'best possible' sequence over the scaffold from only the SOLiD reads.
Is there any way to do this in MAQ or in another package?