Introduction

nfcore/nanoseq is a bioinformatics analysis pipeline that can be used to demultiplex, QC and map Nanopore data.

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. Basecalling, barcoding and adapter trimming (Guppy; optional)
   • Sequencing QC (pycoQC, NanoPlot)
2. FastQ QC (NanoPlot, FastQC)
3. Alignment (GraphMap2 or minimap2)
   • Each sample can be mapped to its own reference genome if multiplexed in this way
   • Convert SAM to co-ordinate sorted BAM and obtain mapping metrics (SAMtools)
4. Create bigWig (BEDTools, bedGraphToBigWig) and bigBed (BEDTools, bedToBigBed) coverage tracks for visualisation
5. Present QC for alignment results (MultiQC)

Quick Start

i. Install nextflow

ii. Install one of docker or singularity

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

nextflow run nf-core/nanoseq -profile test,<docker/singularity/institute>

Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile institute in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

iv. Start running your own analysis!

nextflow run nf-core/nanoseq \
    --input samplesheet.csv \
    --protocol DNA \
    --run_dir ./fast5/ \
    --flowcell FLO-MIN106 \
    --kit SQK-LSK109 \
    --barcode_kit SQK-PBK004 \
    -profile <docker/singularity/institute>

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

Documentation

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

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

Credits

nf-core/nanoseq was originally written by Chelsea Sawyer and Harshil Patel from The Bioinformatics & Biostatistics Group for use at The Francis Crick Institute, London. Laura Wratten from the Genome Institute of Singapore is one of the primary contributors along with Johannes Alneberg and Franziska Bonath from SciLifeLab, Sweden.

Many thanks to others who have helped out along the way too, including (but not limited to): @crickbabs, @AnnaSyme.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on Slack (you can join with this invite).

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.