This repository contains material and instructions for the tutorial detailed in the article Assembly of ancient mitochondrial genomes without a closely related reference sequence by Christoph Hahn in Ancient DNA: Methods and Protocols, Second Edition, edited by Shapiro B., Hofreiter M., Rodrigues Soares A.E., Heintzman P.D., Paijmans L.A., and Barlow A.
Repository is permanently archived at Zenodo:
If you want to run through the tutorial, download this repository, e.g. via:
git clone --recursive https://github.com/chrishah/aMITO_MiMB.gitThen, change your present working directory to the directory tutorial/ in the repo:
cd aMITO_MiMB/tutorial/The tutorial/ directory contains a directory mt_refs that contains the reference data in fasta format needed for the tutorial. Check if everything's there:
ls -1 mt_refs/*.fastaNow, either continue by setting up the required software, as described in the article, or use the Docker image (see here) that we have prepared for the tutorial (recommended). Find out what Docker is here.
The image contains a stripped down version of Ubuntu 16.04 and all necessary executables and dependencies to run the tutorial. Docker is compatible with all major operating systems, including Mac OSX and Windows (see here). The image has been tested on Ubuntu, but it should work without problem in any other system where docker was successfully installed.
Start the docker container by doing (might require sudo):
docker run -i -t -v $(pwd):/home/working --rm --net=host chrishah/amito_mimb /bin/bashThis will download the image, start up the docker container (you will see the prompt change) and mount the directory /home/working (do not change) of the container to your current working directory ($(pwd) - change if you want).
NOTE that the first startup may take a couple of minutes because the above command will first download the image from docker hub. Subsequent launches will take only seconds.
Now, you should be good to go ..