mutation-accumulation-pipeline

A pipeline specifically to process small sequences generated from mutation accumulation experiments. Credit to Nathaniel Sharp and Jacob Roman-Fredette for the general snakemake rule layout and read group shell script.

This pipeline currently does not support multiple-lane sequencing runs for now.

Dependencies

fastqc, BBMap, Trimmomatic, fastq_screen, bwa-mem2, samtools, picard, gatk4

Instructions

1. Install the dependencies using conda.
2. In your working directory, create a pipelines directory and put the pipeline config, readgroup shell script, your fastq_screen config, and the pipeline in there.
3. Create a directory called sequences and move your raw sequencing outputs into a new directory underneath named reads.
4. Create another directory under sequences named adapter, and move the adapters that you used under there.
5. Next, download your species' reference genome under a new directory titled alignment_reference.
6. If you want to screen against suspected contaminants, download reference genomes into a directory named screens.
7. Run the pipeline on -np mode to check if the expected files will be generated.
8. Run the pipeline with the following command: snakemake -s pipeline.smk --cores .