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index.qmd
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Welcome to the Website for the "Ancient DNA Data Analysis" workshop.
# Technical prerequisites
Our interactive exercises require a mix of tools, such as [R](), [samtools](), [Eigensoft]() and [Poseidon]().
If you are an attendee of this workshop, you will have access to a [prepared RStudio-Cloud environment](#rstudio-cloud) which has all that you need ready to go. The only thing you will need is a webbrowser and an RStudio-Cloud account, see below.
## RStudio-Cloud
Our interactive exercises are done in [RStudio-Cloud](https://cloud.rstudio.com).
In order to join our "classroom" workspace, you need to follow [this link](https://rstudio.cloud/spaces/176275/join?access_code=1NmxCT-MoLxxaM6m0jV5sVLJvol_eTvsEYcwDGeX). Then follow these steps:
- Click on "Sign up" to create a free account, _or_, if you already have an account, simply log in
- In the workshop space, you should now see "Join Space?" -> Click "YES"
- In the top menu, click on "Projects"
- You should see a project named "Ancient_DNA_Workshop_Sept_2022". Click on "Start" right next to it.
- You should now see something like this:
# Schedule
## Day 1, Tue, Sept 6
| Time | Activity |
|:--------------|:------------------------------------------------------|
| 13:30 - 15:00 | Introduction
| 15:00 - 15:30 | *Coffee break* |
| 16:00 - 18:00 | Part 1: Sequencing Data
## Day 2, Wed, Sept 7
| Time | Activity |
|:--------------|:---------------------------------|
| 08:30 - 9:30 | Part 2: Neandertals and ghosts |
| 9:30 - 10:00 | *Coffee break* |
| 10:00 - 12:00 | Part 2: Neandertals and ghosts (cont.) |
| 12:00 - 13:00 | *Lunch break* |
| 13:00 - 15:00 | Part 3: Human history during the last 10,000 years |
# Exercises
* [Exercise 1.1: Alignment](exercises/exercise_1_1_alignment.qmd)
* [Exercise 1.2: Visualising BAM files](exercises/exercise_1_2_tview.qmd)
* [Exercise 1.3: Genetic sex determination](exercises/exercise_1_3_sex_determination.qmd)
* [Exercise 2.1: Neandertal admixture in modern humans](exercises/exercise_2_1_abba_baba.qmd)
* [Exercise 3.1: Recent human population structure](exercises/exercise_3_1_PCA.qmd)
## Solutions
* [Solution 1.1](exercises/solution_1_1_alignment.qmd)
# Instructor
[Stephan Schiffels](https://www.eva.mpg.de/archaeogenetics/staff/stephan-schiffels) is a group leader at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. He has originally studied physics and obtained his PhD in 2011. He worked as a Postdoc at the Wellcome Trust Sanger Institute in Hinxton, UK and since 2015 as a group leader at the Max Planck Institute. His research interests range from theoretical population genetics, statistical and bioinformatic method development, to large-scale archaeogenetic studies to investigate the human past.