Assembly With Phrap With Some Missing Quality Files.

Question

[Joseph Hughes]

I am trying to assemble sequences with phrap, for some of the sequences I have the associated quality file but not all of them. I have created a fasta file with all my sequences and another file with all the quality information but phrap is not happy as I have some missing quality information for a couple of the sequences:

FATAL ERROR: Inconsistency between quality file and sequence file

Is there a way I can phrap sequences together even if I have some missing quality information for some of the sequences? How?

Answer 1

[Darked89]

You may try to experiment with fake quality values for these sequences which miss them. One may start with just putting 4s, 10s or anything in between (http://www.phrap.com/phred/) and check if there are big differences in assembly.

More accurate approach (assuming the same sequencing technology/chemistry) would be to calculate average base quality at a given position from reads you have real values, and put these for reads without quality values.

You may also assembly reads with qualities first, then map the remaining ones to existing contigs. Use the mapping quality to estimate quality of the reads (lower the quality for mismatches), but this is probably an overkill.