529053 Evolutionary Genomics
The course took place in spring 2016.
This course will teach efficient use of central tools in computational analysis of high-throughput resequencing data and the theoretical background of the key analyses. The course comprises of lectures and computer exercises. Computer exercises will be performed on personal laptop computers using CSC servers and a tailored Linux virtual machine. The course requires familiarity with Linux command-line work.
Lectures give an introduction to theoretical (population genetic) background of the analysis methods.
- coalescent theory
- effective population size
- drift vs. selection
Computer exercises focus on the peculiarities of working with non-model organisms (nine-spined stickleback in this case) but also include analyses with 1000 Genomes (human) data.
- mapping of short-read data to a reference genome
- variant calling, joint calling, and filtering
- exploratory analyses (PCA, clustering)
- ancestral allele inference using outgroup species
- population structure and history (admixture, Fst, Ne)
- annotation (Ensembl, UCSC) transfer from model species
- data visualisation
The bioinformatic software used include bwa, samtools, bcftools, gatk, plink, last, admixture, stairway-plot and R.
- Lecture: Introduction to the course
- Lecture: Introduction to Genomics
- Setting up the Linux Virtual Machine
- Practical: Using the LinuxVirtual Machine
Theory of short read mapping (by Alan Medlar)
From Fastq to Vcf
Handling Sam and Vcf data, quality control
- Lecture: Handling Sam and Vcf data, quality control
- Practical: Handling Sam and Vcf data, quality control
Genomic alignment, ancestral alleles, lift-over of coordinates
- Lecture: Genomic Alignment, ancestral alleles, lift-over of coordinates
- Practical: Genomic Alignment, ancestral alleles, lift-over of coordinates
- Practical: Derived allele frequencies, annotation liftover
Detecting directional selection (by Tuomas Toivainen)
Visualisation, targeted assembly and Admixture
- Demo: Visualisation of genomic data and Admixture
- Practical: Visualisation of genomic data and Admixture
- Practical: Targeted de novo assembly
Ensembl REST API, Variant Annotation and FFD sites
- Demo: Ensembl REST API, Variant Annotation and FFD sites
- Practical: Ensembl REST API, Variant Annotation and FFD sites
1000 Genomes data and populationhistory