Nanopore demultiplexing, QC and alignment pipeline
*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.
- Basecalling and/or demultiplexing (
- Sequencing QC (
- Raw read QC (
- Alignment (
* 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 (
- 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 <institute>in 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 \ --input_path ./fast5/ \ --flowcell FLO-MIN106 \ --kit SQK-LSK109 \ --barcode_kit SQK-PBK004 \ -profile <docker/singularity/institute>
The nf-core/nanoseq pipeline comes with documentation about the pipeline, found in the
- Pipeline configuration
* Local installation
* Adding your own system config
* Reference genomes
- 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. 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.
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
Citation<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi. --> <!-- If you use nf-core/nanoseq for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
You can cite the
nf-core publication as follows:
*The nf-core framework for community-curated bioinformatics pipelines.*
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.