What are you large contig (> 100 kb) sequencers using to assemble your reads? Do you all use
phrap? Anybody using an assembler that uses forward/reverse read constraints in the assembly
Phrap seems to note where forward/reverse reads have been mis-assembled (ie, assembled facing
away from each other) -- but doesn't seem to change the assembly to correct this.
We sequenced a BAC that had a series of about five 2kb tandem repeats. The repeats are about 99%
identical. Further, this repeat block is flanked by inverted repeats. I wanted to try another
assembly engine to compare to phrap's assembly. So I tried cap3--which does use forward/reverse read
constraints in the assembly process. However cap3 took about 10 times longer to assemble the data
and produced more gaps.
I think quite a few groups use Gap. Which assembly engine do you use with that? (Staden Gap can
use its own assembly engine or cap3, fakII or phrap.)
Purdue Genomics Core Facility