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Assembly engines

Phillip San Miguel pmiguel at purdue.edu
Mon Feb 26 12:23:01 EST 2001


    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
process?
    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.)

Phillip SanMiguel
Purdue Genomics Core Facility


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