ancient_trichuris

Population genomics of ancient and modern Trichuris trichiura

Overview of workflow and code used in the analysis

The code used in this project has been divided into workbooks based on the analysis performed, which are listed below. Each workbook can be accessed using the hyperlinks.

Workbook:Genome analyses

• Reference genome
• Genome completeness using BUSCO
• Transfer of gene models using LiftOff
• Running interproscan on liftoff annotation

Workbook:Mapping

• Project setup
• Prepare reference genome
• Raw sequence data
• metadata
• trimming of the raw reads
• FIX: merge duplicate ancient read sets
• Mapping

Workbook:Kraken

• kraken - modern samples
• kraken - ancient samples

Workbook:DNA damage

• pmdtools
• plot deamination frequencies
• trim bases from reads in bam to remove deamination

Workbook:Genome coverage

• Genome wide coverage
• Generate quantitative stats on coverage for supplementary tables
• generate some coverage plots
• Genome-wide coverage to determine worm sex

Workbook:Variant calling and filtering

• Genome scope to estimate heterozyosity
• GATK
• Filter the VCF - SNPable
• Filter the VCF - hardfilter
• Querying SNP and INDEL QC profiles to determine thresholds for filters
• Applying filters to the variants
• merge VCFs
• Filter genotypes based on depth per genotype
• Sample missingness
• Generate an ALL SITES variant set for running pixy

Workbook:Sampling sites

• World map
• Sampling timepoints
• Map of ancient DNA sites, with Fst data showing degree of connectivity between populations

Workbook:PCAs

• PCA of mitochondrial variants
• PCA of nuclear variants

Workbook:ANGSD

• IBS and Coviance matrices
• Single allele analyses of mitochondrial and nuclear variants

Workbook:NGSadmix

• Admixture plots
• Clumpak to determine optimal K

Workbook:Treemix

• Treemix
• plotting treemix data
• Estimating the optimal number of migration edges
• calculate the variance explained by the data

Workbook:Admixtools

• Prepared data and run admixtools
• plotting admix data

Workbook:Population history using SMC++

• run smc++
• plot all smcpp plots together

Workbook:Genome-wide genetic variation

• Running pixy to calculate nucleotide diversity, dXY and Fst between groups
• analyses of nucleotide diversity (Pi)
• dXY and Fst
• extracting top X% of Fst values for each comparison
• Private and shared variation between populations
• Ancient DNA - nucleotide diversity vs sampling age
• Sample Heterozygosity vs sequencing coverage
• Relatedness and kinship between samples in a population
• genome-wide analyses presented in the original draft of the manuscript

Workbook:Beta-tubulin variation

• Analysis of variation within beta tubulin
• Reanalysis of nucleotide diversity around beta-tubulin