Nanopore analysis

Quality control, Basecalling and multiplexing of sequencing reads generated by Oxford Nanopore sequencers.

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.

When we run analysis

At NGI Stockholm we run this analysis routinely for internal and development projects as our basic Nanopore QC pipeline and for demultiplexing. Although the pipeline is also able to map the reads to a reference, we currently do not use this feature internally.

If you would like us to run this pipeline for data generated at NGI Uppsala, please get in touch and mention that you would like us to run this analysis. Decisions, whether we take on a specific project, are made on a case-by-case basis.

Input data

  • fast5 files (raw files generated in MinKnow)
  • sample sheet (specifying sample name and Nanopore index)
  • basic information about
    • barcode kit
    • library preparation kit
    • flow cell type
  • (optional) reference genome


  • FastQ files, separated by Nanopore index (basecalling performed by Guppy)
  • PycoQC report
  • NanoPlot report

Last Updated: 24th March 2022

Please read our sample submission instructions before sending samples:

Sample Submission Guidelines
Method Status


We are currently testing this method. Please contact us to find out more.

Software tool versions

View all software versions

Compatible Methods