Home Pre-workhop Instructions
Lectures
1: Introduction and Key Concepts 2: Variant Detection and Phylogenetic Trees 3: Practical Applications of WGS and Phylogenetics 4: Advanced Applications of WGS
Practical 1: WGS Data Analysis
Obtaining sequencing data Viewing raw sequencing data QC of FASTQ files Cleaning and filtering FASTQs Reference mapping/alignment De novo assembly
Practical 2: Variant Calling and ML Trees
Variant calling and VCFs Building consensus sequences Aligning consensus sequences Maximum Likelihood trees
Practical 3: Timed Phylogenetic Trees
ML timed trees Bayesian trees (Bactdaing) Bayesian trees (BEAST2)
Practical 4: Transmission and Profiling
Identifying lineages and serotypes Transmission network reconstruction
Practical 5: Mixed Infection, Recombination and ANI
Identifying mixed infection Detecting recombination Average nucleotide identity (ANI)
Practical 6: Phylogeography and Phylodynamics
Phylogeography Inferring population dynamics
Practical 7: Fitness and Selection
Local branching index (LBI) Detecing homoplasy dN/dS GWAS


Solution to masking sites:

require(seqinr)
B117_aligned<-seqinr::read.fasta("Taiwan_B117_aligned.fasta",forceDNAtolower = F)
mask_positions<-c(1:264,29674:29903)
newfasta<-lapply(1:length(B117_aligned), function(x){replace(B117_aligned[[x]],mask_positions,"N")})
names(newfasta)<-names(B117_aligned)
seqinr::write.fasta(newfasta,names(newfasta),"Taiwan_B117_aligned_masked.fasta",open = "w")

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