nfcore/nanoseq repository overview

⁠Introduction

nfcore/nanoseq is a bioinformatics analysis pipeline that can be used to perform basecalling, demultiplexing, mapping and QC of Nanopore DNA/RNA sequencing 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 and/or demultiplexing (Guppy⁠ or qcat⁠; optional)
2. Sequencing QC (pycoQC⁠, NanoPlot⁠)
3. Raw read QC (NanoPlot⁠, FastQC⁠)
4. Alignment (GraphMap2⁠ or minimap2⁠)
   • Both aligners are capable of performing unspliced and spliced alignment. Sensible defaults will be applied automatically based on a combination of the input data and user-specified parameters
   • 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)
5. Create bigWig (BEDTools⁠, bedGraphToBigWig⁠) and bigBed (BEDTools⁠, bedToBigBed⁠) coverage tracks for visualisation
6. Present QC for alignment results (MultiQC⁠)

⁠Quick Start

1. Install nextflow⁠

2. Install one of docker⁠ or singularity⁠

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

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

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   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.

4. Start running your own analysis!

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

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See usage docs⁠ for all of the available options when running the pipeline. An example input samplesheet for performing both basecalling and demultiplexing can be found here⁠.

⁠Documentation

The nf-core/nanoseq pipeline comes with documentation about the pipeline which you can read at https://nf-core/nanoseq/docs⁠ or find in the docs/ directory⁠.

⁠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. Other primary contributors include Laura Wratten⁠, Chen Ying⁠ and Jonathan Goeke⁠ from the Genome Institute of Singapore⁠, 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 the Slack #nanoseq channel⁠ (you can join with this invite⁠).

⁠Citation

If you use nf-core/nanoseq for your analysis, please cite it using the following doi: 10.5281/zenodo.3697959⁠

You can cite the nf-core publication as follows: