diet_calculus

This repository describes the analysis performed in the paper Mann et al. 2020. Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus. Quaternary International

Setup

This repository assumes you are running in a Unix environment (e.g. Mac OSX or Linux) and you have conda installed.

To get this repository:

• Install and set up up anaconda or miniconda as described at the bioconda documentation, including setting up channels.
• Clone this repository to your machine and change into the directory with

git clone https://github.com/aemann01/diet_calculus.git && cd diet_calculus/

• Run the following command to install the one of the environments

conda env create -f environment.yml

• To load a given environment run

conda activate mann2020_<analysis_name>

• To turn off the environment run

conda deactivate

Structure

This repository contains a directory for each analysis.

Within each directories a Conda environment.yaml file for the particular analysis' software, a README describing the procedure of analysis, and intermediate and results files. Note that some intermediate files are not contained here due to large sizes (e.g. raw sequencing data and databases).

01-example_mapdamage

02-damage_downscaling

03-synthetic_dataset_generation

04-synthetic_dataset_processing

05-taxonomic_profiling