# BB-QTL Inference Pipelines
This repo accompanies the research article "Barcoded Bulk QTL mapping reveals highly
polygenic and epistatic architecture of complex traits in yeast" by Nguyen Ba AN, 
Lawrence KM, Rego-Costa A, Gopalakrishnan S, Temko D, Michor F, and Desai M (2021).

It contains example pipelines and minimal code necessary for:
1. processing of raw sequencing reads into inferred genotype and phenotype data;
1. inference of QTLs from genotype and phenotype data under additive and epistatic models.

The code is not expected to be readily functional to the user, as dependencies, paths and 
hardcoded values would need to be appropriately adjusted.

Raw sequencing reads were uploaded to NCBI SRA under accession PRJNA767876.

The final inferred genotype and phenotype data are deposited in:
Nguyen Ba AM, Lawrence KM, Rego-Costa A, Gopalakrishnan S, Temko D, Michor F, Desai M, 2021, 
"Barcoded Bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast", 
https://datadryad.org/stash/share/-NXjYqEJrSJcSWn1t7GsZ0YPIdO-l9CK8kvPw9ndxH8, 
Dryad Digital Repository, doi:10.5061/dryad.1rn8pk0vd

The final QTL models are included as supplementary files together with the published research article.