Assembly of multiple BACs

[nelsonwd]

I'm new to this so I'm hoping this is a basic question and that someone can suggest a good reference to guide me.

I have 6 lanes of Illumina 100mer paired-end data representing 6 BACs from a plant chromosome (no reference sequence). 5 0f the 6 BACs should overlap.
I have assembled the 6 BACs separately using velvet.
I was then hoping to assemble the velvet contigs.fasta of the BACs using a tool like the Staden package or PHRAP/Consed but have just realized that I'm not sure how to do this and keep the scaffolding and quality scores. What is the most common strategy for assembling a set of BACs?

1)Should I have assembled all 6 BACs (or the 5 overlapping BACs) together?
2)Should I have used the velvetg -amos_file option and then used the AMOS suit?(just starting to read about AMOS)

Thanks,
Bill

[krobison]

Are you masking out reads with vector sequence in them? Otherwise, they may assemble oddly if you try to assemble them together in one go?

Even if you didn't generate an AMOS file, it is straightforward to merge contigs (once you clip out the vector) using minimus2 (part of the AMOS suite).

[nelsonwd]

Thanks, I'll try minimus2 tomorrow.