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Old 09-09-2021, 05:16 AM   #1
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Location: Copenhagen, Denmark

Join Date: Feb 2011
Posts: 5
Red face SNP Bacterial Genomes per year

I am looking at SNP trees for bacterial genomes (mostly N. gonorrhoeae, S. aureus and E. faecium) and I am following outbreaks in society and on hospital wards.
Do you know the number of SNPs that will appear per year for the different species, and where I can find some information about that.
Best Regards
Peder Worning
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Old 09-22-2021, 01:08 AM   #2
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Location: United Kingdom

Join Date: Sep 2021
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You want probably want to use snpRelate for this, seeing as you only have the vcfs.

But, hypothetically there are tools that will let you turn vcf +reference files to a contig so the process is Vcfs->fastas(the contigs for all vcfs)-mafft(an multiple sequence aligner)> msa.fa -phyml-> phylogenetic tree
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Last edited by Bjork; 01-25-2022 at 03:21 AM.
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bacteria, genomes, snp, time, year

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