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.
- Basecalling, barcoding and adapter trimming (
- FastQ QC (
- Alignment (
- 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 (
- Create bigWig (
bedGraphToBigWig) and bigBed (
bedToBigBed) coverage tracks for visualisation
- Present QC for alignment results (
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 institutein your command. This will enable either
singularityand 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.
The nf-core/nanoseq pipeline comes with documentation about the pipeline, found in the
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
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.
If you would like to contribute to this pipeline, please see the contributing guidelines.
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.