SheepTreeSeq: Scalable analysis of sheep genome diversity using tree sequences

The aim of this project is to analyze the sheep genome diversity using tskit TreeSequence files. In this context data from Whole Genome Sequencing (WGS) and data from SNPchips will be analyzed.

Setting up the environment

• Project Setup
• Build the documentation

Introducing TreeSequences

• Quickstart
• Getting started with tskit
• TSINFER tutorial
• TSINFER with SMARTER test data
• Inference from a test VCF file

Simulating TreeSequences

• Analyze the simulated data
• Test TreeSequences with different mutation rates
• Dataset for TS inference
• Explore threads metadata
• Threads fitting data

The SMARTER database

• The SMARTER-database
• Get SMARTER samples list
• Infer ancestry using EST-SFS
• Reading data from chromosome 26
• Nucleotide diversity
• About tstree space
• Get ancient information from ensemble compara
• SMARTER 50K
• 50K simulations results
• Population statistics
• Population statistics plots