How to generate WGS Multiple sequence alignment file

Question

[Optimist]

Can you please help me tools that can be used to generate an alignment file using 16 bacterial whole genome sequences. Size of the genomes varies between 3.8 Mb to 4.2 Mb.

I need the alignment file generated by Multiple Sequence aligner as an input for gubbins tool.

Which tool can be used for achieving this purpose?

Thanks a ton

[andres.firrincieli]

Hi,

I am not familiar with gubbins but as stated in the github page you can use snippy . Keep in mind that your genomes must be almost identical to the reference genome: link