[AMOS-help] 454 assembly using CA, why do I see scaffolds?

[Dan B. <dan...@gm...>]

Hi, I'm running an assembly using the Celera Assembler on a large set
of 454 reads. The assembly seems to run fine, but in the output (in
hawkeye) I'm seeing several scaffolds. I was wondering why there are
any scaffolds in the data, as the reads are all single end with no
mate-pair information. Could my <file>.seq / <file>.qual import
pipeline be leading to incorrect identification of libraries and mate
pairs?

Sorry for the basic question, but I just don't see why scaffolds are
being produced otherwise.

Cheers,
Dan.