I try to compare assembled genomes (contigs in a multi fasta file) against a reference genome (complete genome in 1 fasta entry). I thought to use BRIG but I don't have any results. When I give the multi fasta file as the query, nothing is printed on the picture. I only get the reference and nothing else.
There is no information about using a multi fasta file as query in the BRIG manual. Does anyone have an idea how I can make it work? Is it doable? Or should I use another software?
Thanks a lot,