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week 5 SNP Phylogeny for outbreak investigation - Coggle Diagram
week 5 SNP Phylogeny for outbreak investigation
Call Single Nucleotide Polymorphisms (SNPs)
BCF
VCF
definition of the format: insert here
Investigation of Foodborne outbreaks in Denmark
Single Nucleotide Polymorphism Phylogeny
Being able to trace back where the outbreak comes from
Calling SNPs and Inferring
Phylogenies
Single Nucleotide Polymorphism Phylogeny
Make pseudo-alignment
reference nucleotides
CALLED SNPS
Infer phylogeny
Maximum likelihood
Most accurate
Can’t provide SNP distances
Maximum Parsimony (Minimum evolution)
Intuitive method
Underestimates actual evolutionary change (LBA)
Provides SNP distances
Popular substitution models
Kimura 80 (K80)
Hasegegawa - Kishino - Yano (HKY)
Jukes-Cantor (JC69)
Generalised Time Reversible (GTR/REV)
Markov models
Used to calculate likelihood of phylogenetic trees
Find differences (SNP calling), compared to a reference sequence. - Close reference is better (No cross species analysis)
Alignment to Reference
Assumption: random + indenpendent
Additional Steps & Limitations
Limitations
SNPs are not random & independent
Diversity => Less confidence
Additional steps
Remove/Handle non-core SNPs
Further filtering
Pruning – Remove SNPs caused by mobile elements