Hello,
I have three bacterial genomes (~ 4 Mb), all strains of the same species. One has already been published and will serve as a reference genome for my study.
How do I find the copy number variation and also the synteny variation in these? Not sure what programs to use. I've had a look at Geneorder4.0 but the online tool doesnt let me convert my genebank files to the required format, so I havent been successful in using it yet.
I know basic linux, and can use programs like soapdenovo, velvet, bwa etc.
Please help!
bgansw
I have three bacterial genomes (~ 4 Mb), all strains of the same species. One has already been published and will serve as a reference genome for my study.
How do I find the copy number variation and also the synteny variation in these? Not sure what programs to use. I've had a look at Geneorder4.0 but the online tool doesnt let me convert my genebank files to the required format, so I havent been successful in using it yet.
I know basic linux, and can use programs like soapdenovo, velvet, bwa etc.
Please help!
bgansw