RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding
Emily Humble, Kanchon K Dasmahapatra, Alvaro Martinez-Barrio, Ines Gregorio, Jaume Forcada, Ann-Christin Polikeit, Simon D Goldsworthy, Michael E Goebel, Joern Kalinowski, Jochen Wolf and Joseph Hoffman
This repository contains the main code and data used in the manuscript.
Manuscript available here
snp_discovery_pipeline_PILONGENOME_Nov2017.sh : documented workflow for SNP discovery
alignment_notes_Nov2017.sh : documented workflow for the genome alignment
R scripts contain the code for the main analysis workflow
/R contains some R functions used in the pipeline
/data/raw contains some necessary raw data files for the analysis
/data/processed is necessary for storing any intermediate output files
/scripts contains some R and bash scripts necessary for the analysis
Image: John Dickens