Rabbits

This repository contains Python and R code for processing data, running analyses and plotting figures from the paper Rabbits and the Specious Origins of Domestication

If you reuse any of this code then please cite the paper:

Irving-Pease, E.K., Frantz, L.A.F., Sykes, N., Callou, C., Larson, G., 2018. Rabbits and the Specious Origins of Domestication. Trends in Ecology & Evolution 33, 149–152. https://doi.org/10.1016/j.tree.2017.12.009

Installation

To reproduce the analyses from the paper you will need to install the following dependencies.

Python

Python ≥ 2.7 with the following modules:

• dadi
• luigi
• matplotlib
• numpy

pip install luigi matplotlib numpy 

pip install git+https://bitbucket.org/gutenkunstlab/dadi.git

The full list of Python modules installed in the project environment can be found in the requirement.txt file.

R

R ≥ 3.4 with the following modules:

• ape
• ggplot2
• mapdata
• maps
• reshape2
• scales
• stringr

install.packages(c("ape", "ggplot2", "mapdata", "maps", "reshape2", "scales", "splancs", "stringr"))

Other

• SRA Toolkit
• Samtools
• Picard
• BWA
• GATK
• Plink
• ADMIXTURE
• sNMF
• FlashPCA

Running the pipeline

The pipeline is broken into two luigi modules.

Pre-processing

• download the data from the SRA and Ensembl
• align the data with BWA
• sort and merge with Samtools
• deduplicate with Picard
• variant call and filter with GATK
• convert to Plink
• run ADMIXTURE and sNMF
• run FlashPCA
• plot NJ tree

luigi --module pipeline_gatk CustomGenomePipeline

Fitting ∂a∂i models

• compute the SFS
• fit ∂a∂i models

luigi --module pipeline_dadi CustomDadiPipeline

Author

Evan K. Irving-Pease, PalaeoBARN, University of Oxford

License

This project is licensed under the MIT License - see the LICENSE.md file for details