I have ~40 permanent draft bacterial genomes, and I've already obtained their core genes.
I know I could use MAUVE to align the genomes and find the SNPs; however, I don't have a powerful enough computer to do that.
So is there a way to do it in a less computational-heavy way? Command line programs are fine.
And, do I definitely need a reference genome when calling SNPs within these ~40 bacterial genomes? I mean, I have identified the variable nucleotides for the core genes, but I cannot say they are SNPs unless I compare them to a reference, right? However, it seems that when one uses MAUVE to align genomes and call SNPS, one does not have to include a reference genome in the alignment.
Thanks a lot for your help.
I know I could use MAUVE to align the genomes and find the SNPs; however, I don't have a powerful enough computer to do that.
So is there a way to do it in a less computational-heavy way? Command line programs are fine.
And, do I definitely need a reference genome when calling SNPs within these ~40 bacterial genomes? I mean, I have identified the variable nucleotides for the core genes, but I cannot say they are SNPs unless I compare them to a reference, right? However, it seems that when one uses MAUVE to align genomes and call SNPS, one does not have to include a reference genome in the alignment.
Thanks a lot for your help.
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