/pipelines2020

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pipelines2020

intro to population genomics

1. HPC intro, genotyping pipelines, PCA - Acropora millepora coral

slides: TACC intro, genotyping

slides: Pop structure

A. millepora under fluorescent microscope

Walkthrough: pipelines_day1_QC_PCA_admixture.sh

Scripts:

  • OKall_ibs.R
  • OK_ibs.R
  • admixturePlotting_pcangsd.R
  • admixturePlotting_v5.R

Files from precomputed results directory (in case you get stuck):

  • dd.pdf: quality control plots
  • OKall_ibs.R : initial IBS matrix
  • OKall_ibs.R : final IBS matrix
  • bams.nc : filtered bam list
  • pcangsd* : several files containing PCAngsd output

2. Allele Frequency Spectra, demographic modeling

slides

Walkthrough: pipelines_day2_AFS.sh

3. Do-it-yourself! Idotea baltica project

Idotea baltica

bams: /work/01211/cmonstr/IB/recal_bams

metadata: https://www.dropbox.com/s/af5ggl5p7gtuccp/Idotea%20environment%20171005.csv?dl=0