SNP Bacterial Genomes per year

pederworning · 09-09-2021, 05:16 AM

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

Bjork · 09-22-2021, 01:08 AM

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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09-09-2021, 05:16 AM	#1
pederworning Junior Member Location: Copenhagen, Denmark Join Date: Feb 2011 Posts: 5	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

09-22-2021, 01:08 AM	#2
Bjork Junior Member Location: United Kingdom Join Date: Sep 2021 Posts: 1	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 __________________ minotaurfightstore \| minotaurfightstore Last edited by Bjork; 01-25-2022 at 03:21 AM.