Skip to content
@epi2me-labs

EPI2ME

Bioinformatics resources from Oxford Nanopore Technologies Plc

EPI2ME Labs

Welcome to the EPI2ME GitHub organization! We develop and maintain open-source bioinformatics tools and workflows for Oxford Nanopore Technologies' data analysis.

About EPI2ME on GitHub

EPI2ME is a collection of bioinformatics tools, workflows, and resources designed to help researchers analyze nanopore sequencing data. Our projects focus on making cutting-edge analysis accessible and reproducible for the scientific community.

Our Tools and Workflows

We provide a variety of tools and workflows for:

  • Nextflow workflows: Production-ready bioinformatics pipelines
  • Utility tools: Command-line tools and libraries for nanopore data processing
  • Community resources: Documentation, tutorials, and examples

Getting Started

Visit epi2me.nanoporetech.com to explore our workflows and documentation.

Support

For questions and support:

Please note that repositories in this organization may not be proactively monitored for support requests. For more timely assistance, please use the resources above.

License

Individual repositories may have different licenses. Please refer to each repository's LICENSE file for specific terms.

Pinned Loading

  1. kraken2-server kraken2-server Public

    Kraken2 Server

    C++ 23 4

  2. wf-transcriptomes wf-transcriptomes Public

    Nextflow 110 46

  3. wf-single-cell wf-single-cell Public

    Python 104 47

  4. wf-bacterial-genomes wf-bacterial-genomes Public

    Small variant calling for haploid samples

    Python 48 20

  5. wf-human-variation wf-human-variation Public

    Nextflow 150 76

  6. fastcat fastcat Public

    Simple utility to concatenate .fastq(.gz) files whilst creating a summary of the sequences.

    C 51 4

Repositories

Showing 10 of 30 repositories
  • wf-flu Public
    epi2me-labs/wf-flu’s past year of commit activity
    Python 21 7 3 0 Updated Jan 23, 2026
  • epi2me-labs/wf-single-cell’s past year of commit activity
    Python 104 47 15 1 Updated Jan 23, 2026
  • wf-16s Public
    epi2me-labs/wf-16s’s past year of commit activity
    Nextflow 42 6 1 0 Updated Jan 23, 2026
  • wf-metagenomics Public

    Metagenomic classification of long-read sequencing data

    epi2me-labs/wf-metagenomics’s past year of commit activity
    Python 100 32 2 0 Updated Jan 22, 2026
  • epi2me-labs/wf-human-variation’s past year of commit activity
    Nextflow 150 76 13 0 Updated Jan 22, 2026
  • wf-bacterial-genomes Public

    Small variant calling for haploid samples

    epi2me-labs/wf-bacterial-genomes’s past year of commit activity
    Python 48 20 6 0 Updated Jan 5, 2026
  • wf-aav-qc Public
    epi2me-labs/wf-aav-qc’s past year of commit activity
    Python 8 11 2 0 Updated Dec 17, 2025
  • wf-teloseq Public
    epi2me-labs/wf-teloseq’s past year of commit activity
    Python 5 1 0 0 Updated Dec 16, 2025
  • wf-amplicon Public
    epi2me-labs/wf-amplicon’s past year of commit activity
    Python 41 13 1 0 Updated Dec 15, 2025
  • epi2me-labs/wf-basecalling’s past year of commit activity
    Nextflow 48 27 10 1 Updated Dec 15, 2025

Most used topics

Loading…