Go Back   SEQanswers > General

Similar Threads
Thread Thread Starter Forum Replies Last Post
SNP detection in Draft genomes ramyag03 Ion Torrent 0 06-13-2015 09:03 AM
new BGI sequencer can sequence 1mil genomes/year ymc MGISEQ (FKA Complete Genomics) 9 03-02-2015 09:43 AM
Any way to check if a SNP is present in 1000 genomes yuanzhi Bioinformatics 3 10-09-2010 09:23 AM
3-year Post-doc in London on mammal genomes steverossiter Academic/Non-Profit Jobs 0 10-08-2010 02:54 AM

Thread Tools
Old 09-09-2021, 06:16 AM   #1
Junior Member
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
pederworning is offline   Reply With Quote
Old 09-22-2021, 02:08 AM   #2
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
Bjork is offline   Reply With Quote

bacteria, genomes, snp, time, year

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:51 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO