This repository contains a series of scripts for calling and annotating mutations from whole-population Illumina sequencing data from multiple time points of an evolution experiment. It is a simplified version of the pipeline used by McDonald, Rice, and Desai (2016). The pipeline takes a set of .fastq files containing raw sequencing reads, aligns them to a reference genome, calls candidate mutations, and filters them for likely mutations. The file pipeline.sh contains a series of bash commands, which submit Slurm jobs, run software, and execute scripts contained in the src/ directory. Because it contains many steps, some of which are resource-intensive and submitted as batch jobs, this script should be executed line-by-line rather than all at once.
Batch jobs are submitted to the Slurm scheduler. If using LSF or another scheduler, you will have to write new submission scripts. If using Slurm, please make sure that the partition and other Slurm variables are appropriate for your cluster. You can find these variables in the various .slurm scripts.
The following software is used in the pipeline.
python-2.7bowtie2-2.1.0: align reads to reference sequencesamtools-0.1.19: handling .bam filespicard-tools-1.44: marking duplicate reads- GATK
UnifiedGenotyper: run on permissive settings to call candidate mutations
Daniel P. Rice created the pipeline and wrote all scripts - dp-rice.
This project is licensed under the MIT License - see the LICENSE file for details.