How to get complete consensus genome from ordered contigs developed from Mauve?

[hellsingwyk]

Dear all,

I am working on de novo assembly in order to get the whole target genome sequence for phylogenetic analysis.

And now I successfully run velvet to obtain contigs and reorder those contigs using Mauve ---- a java based GUI tools with the help of reference sequence.

However, I have no idea on retrieving complete target genome sequence (consensus sequence). Could anyone give me a hand?

Thank you very much for your kind attention!!!

Best Regards
Michael

[hellsingwyk]

Dear all,

I really have no idea on it and now I only have reordered contigs and have no idea on draft genome development.........

Could anyone give me a hand??

[GenoMax]

If you used progressiveMauve to generate the alignments then there may be (.xmfa) format alignment files in the directory you did the work in. If they are not there you may have to run mauve on the command line (http://darlinglab.org/mauve/user-gui...sivemauve.html).

Once you have the alignment files you can use this script http://www.bioperl.org/wiki/Converting_alignment_files (latest versions is supposed to be here: https://github.com/lskatz/lskScripts to convert .xmfa files to fasta.

[hellsingwyk]

Thank you very much!!!
Let me try try it first~