Physical map-assisted whole genome shotgun assembly

[juckdnarocks]

Hi all,

My question is how to intergrate BAC-end senquencing reads with contigs from WGS. Is there any tools can do this job ?
I have a phyical map with BAC-end sequencing reads , BAC contig orders from BAC fingerprint, and some contigs of assembly result from WGS.

[jimmybee]

Are the BAC contigs from Fingerprints (ie. Physical Contigs) ordered?

My guess would be that if you have a physical map that has been constructed and ordered along chromosome scaffolds, then you would have all BAC locations along your physical map. This means that you can just match the BAC address of the BAC-end sequence (the read names should match) and then anchor WGS contigs to that.

Unfortunately there are no real tools to do this, but it is easily done using a small script and BLAST. You need to match BAC-ends to BACs within the physical contigs, and then use BLAST to match BAC-end sequences to a WGS contig