we have sequence a plant genome through SOLEXA, the reads were assembly into contigs or scaffolds using short read assembler like velvet/soapdenovo etc. however, the scaffold assembled by these assembler is very small, the max scaffold is about 200k in size. we have build a physical map through BAC-fingerprint techniques, and several BAC-END sequence is available for these mapped BACs.
Now i try to map the SOLEXA assembled scaffolds onto the FPC map, using scaffold to BAC-END sequence relationships.
This process is very complicate, i guess if there are tools that can do this job. which link scaffolds through physical map informations.
I found that one tool BAMBUS seems to fulfill my need, but this tool need sequence contig informations in ACE format, which is not available in my current project.
Any suggestions would be appreciated.