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xavierdidelot / ClonalFrameML

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
GNU General Public License v3.0
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how to create the msa file for fragmented genomes #147

Closed jianshu93 closed 1 year ago

jianshu93 commented 1 year ago

Dear ClonalFrameML team,

I my case, my closely related genomes are not in just one piece (linear) but in several pieces because they were from mix sequencing (many other species also in the sample) or not enough coverage to assembly the genome into just one single long piece. How do I generate the msa fasta file as input to ClobalFrameML? I guess I have to use the XMFA format?

Thanks,

Jianshu

xavierdidelot commented 1 year ago

Hi Jianshu,

If you have only a few pieces and that together they cover most of a reference genome, then you could use this reference genome to order the pieces and leave gaps between pieces. But if you have many pieces and/or that they only cover less than say 75% of a reference genome then you should indeed create a xmfa input file which includes each piece separately. See other closed issues on the matter.

Best wishes, Xavier