UK strain competition

This project describes the analysis for the next-generation sequencing data in this study: Human organoid systems reveal in vitro correlates of fitness for SARS-CoV-2 B.1.1.7. Raw sequencing data can be found in BioProject PRJNA722947.

Create working environment

Pre-requisites, using conda to create the working environment:

conda env create -f env.yml

Data

All paired-end fastq files (naming as *_L001_R1.fastq.gz and *L001_R2.fastq.gz) go into the folder data

Analysis

Running the pipeline:

cd codes
conda activate UK_sars
snakemake -s pipeline.smk -p  --config PROJECTPATH=$(dirname $(pwd))