Genome alignments

[astat]

Hello! My question is on how to make a "fake" reference genome from a set of contigs. I have the following data available:

-Assembled contigs from my species (from genomic data, but I only have the contigs)
-A reference genome (different species)
-Linkage maps for both

I would like to make an alignment between the contigs from my species and the reference, then concatenate the contigs from my species into a fake genome based on the order in the reference and/or linkage maps. The contigs are long (several kb), and I expect there to be many gaps due to introns, repeats, etc.

Any suggestions for where to start? Thanks!

[maasha]

Take a look at Mummer for making the alignments.

[lh3]

For mammalian genomes, bwa-sw.