Hi all,
Forgive me if this had been asked before. Here is my question:
I am going to use mauve to make a multiple genome alignment figure. I have one reference genome and four assembled draft genome contigs. If I simply do the multiple alignment all together, the final figure was mess.
Then I am thinking to do the config reordering for every draft genome, based on the reference. Then use four reordered contig files to do the alignment against reference to generate the final figure.
I am not sure if this is a good solution for my goal. Any comment is welcome. But at the moment, when I finished contig reorder, there wasn't a reordered contig file under the result folder, only alignment and .tab file and index file. Is there a way to generate reordered contig fasta?
I appreciate any of your suggestion. Thanks!
Alice
Forgive me if this had been asked before. Here is my question:
I am going to use mauve to make a multiple genome alignment figure. I have one reference genome and four assembled draft genome contigs. If I simply do the multiple alignment all together, the final figure was mess.
Then I am thinking to do the config reordering for every draft genome, based on the reference. Then use four reordered contig files to do the alignment against reference to generate the final figure.
I am not sure if this is a good solution for my goal. Any comment is welcome. But at the moment, when I finished contig reorder, there wasn't a reordered contig file under the result folder, only alignment and .tab file and index file. Is there a way to generate reordered contig fasta?
I appreciate any of your suggestion. Thanks!
Alice