Hi all, I'm trying to perform a global synteny comparison by MAUVE software, between several genomes from NCBI and my draft genome, then I don't know the correct order of my assembled scafffolds, If you have any idea about, I'll be grateful..
I aligned two draft genomes using muave, In my situation the first one is in contig level and the other was in scaffolds level, i divided the two genomes into 20M chunks and make N*M comparisons on mauve where N is the number of chunks in the contigs genome and M is the number of chunks in the scaffolds genome , after that i processed the backbone files,mauve output, to get my desired results.
I used Amazon infrastructure it took about 30 Min to align the two chunks(20M),
My notes on mauve:
I used progressive mauve it is more suitable
Mauve uses alot of temporary files and --scratch parameter dont work for me and it sometimes dont delete theses temp files.
Muave skip characters other Nucleotides as if they didnt exists which will make the indexes in the output misleading
I think you should match all your scaffolds against the NCBI genome and process the backbone output to get the best matching location on the NCBI genome . and you can get more information about the relative positions of your scaffolds,
You can also use something like blat to map you scaffolds, or to just reduce your search space.