Introduction

nfcore/sgrnaquant is a bioinformatics analysis pipeline used for the quantification of CRISPR sgRNA guides obtained from Illumina sequencing.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Pipeline summary

1. Raw read QC (FastQC)
2. Adapter trimming (cutadapt)
3. Alignment (BWA)
4. Count reads and split by strand after filtering (Pysam to remove:
   1. reads that are unmapped
   2. reads that map to multiple guides
   3. reads containing > 0 mismatches
5. Present QC for raw read, alignment and filtering results (MultiQC)

Quick Start

i. Install nextflow

ii. Install one of docker, singularity or conda

iii. Download the pipeline and test it on a minimal dataset with a single command

nextflow run nf-core/sgrnaquant -profile test,<docker/singularity/conda>

iv. Start running your own analysis!

nextflow run nf-core/sgrnaquant -profile <docker/singularity/conda> --design design.csv

See usage docs for all of the available options when running the pipeline.

Documentation

The nf-core/sgrnaquant pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation
2. Pipeline configuration
   • Local installation
   • Adding your own system config
3. Running the pipeline
4. Output and how to interpret the results
5. Troubleshooting

Credits

The pipeline was originally written by The Bioinformatics & Biostatistics Group for use at The Francis Crick Institute, London.

The pipeline was developed by Harshil Patel.

Citation

You can cite the nf-core pre-print as follows:
Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. nf-core: Community curated bioinformatics pipelines. bioRxiv. 2019. p. 610741. doi: 10.1101/610741.