Population Genomics Course: Difference between revisions
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#Data: cp26.ss.fas | #Data: cp26.ss.fas | ||
#Convert to LDhat file format: <pre pre style="white-space: pre-wrap;">../ldhat/convert -seq cp26.ss.fas -2only -prefix cp26</pre> | #Convert to LDhat file format: <pre pre style="white-space: pre-wrap;">../ldhat/convert -seq cp26.ss.fas -2only -prefix cp26</pre> | ||
#Generate likelihood lookup table: <pre pre style="white-space: pre-wrap;">../ldhat/lkgen -lk lk_n100_t0.01 -nseq 14; mv new_lk.txt lk_n14_t0.01</pre> | |||
#In RStudio: <pre pre style="white-space: pre-wrap;">source("http://ldhat.sourceforge.net/R/coalescent.r")</pre> | #In RStudio: <pre pre style="white-space: pre-wrap;">source("http://ldhat.sourceforge.net/R/coalescent.r")</pre> | ||
Revision as of 18:38, 23 June 2013
Learning Goals
- Identification of lineage-specific genomic changes of pathogens
- Estimate recombination, mutation, and selection in natural pathogen populations
Learning outcomes
- Be able to construct genome trees using genome-wide SNPs
- Use genome trees to identify orthologs and paralogs, and gene gains and losses
- Detecting recombination among bacterial genomes
- Use of coalescence tree to describe process of microbial genome evolution
Syllabus
Part 1. Introduction & Overview
- Lecture: 8:30-9:30
- Population processes
- Recombination: Muller's Rachet; Hill-Roberson effect
- Recombination and natural selection: Background selection & selective sweeps
- Applications
- GWAS
- Population history: phylogeny, structuring, gene flow, and selective sweeps (e.g., Neandertal genomes; Borrelia burgdorferi in Northeast US)
- Genomic surveillance of infectious diseases
- Bioinformatics pipeline/protocol
- In-Class Exercise: Software setup & data download
Part 2. Building genome phylogeny/Geographic structuring/Population growth?
- In-class exercise: 10:00-11:30
- Data set: cp26 plasmids from 23 B. burgdorferi sensu lato genomes
- Genome alignment: MUGSY & Alignment viewer: Gmaj
- Genome tree: FastTree
- Tree re-rooting: R package APE see syllabus
- Interactive tree viewer: trexonline
Part 3. Estimation of recombination rate
- In-class exercise: 2-3
- Data set: three pairs of sister-group cp26 plasmids
- LDhat: Instructions; PDF Manual
- Download and Install:
svn checkout https://ldhat.svn.sourceforge.net/svnroot/ldhat; make; make clean
- Data: cp26.ss.fas
- Convert to LDhat file format:
../ldhat/convert -seq cp26.ss.fas -2only -prefix cp26
- Generate likelihood lookup table:
../ldhat/lkgen -lk lk_n100_t0.01 -nseq 14; mv new_lk.txt lk_n14_t0.01
- In RStudio:
source("http://ldhat.sourceforge.net/R/coalescent.r")
- Own script for sister-group counts? (D statistics)
Part 4. Simulation of natural selection & Summary
- In-class exercise: 3:30-5
- ms, seq-gen; Genomes
- BacSim