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@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.

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  1. kraken2-server kraken2-server Public

    Kraken2 Server

    C++ 23 6

  2. wf-transcriptomes wf-transcriptomes Public

    Python 116 51

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

    End-to-end analysis of Oxford Nanopore single-cell sequencing, from barcode and UMI identification to gene and transcript expression

    Python 122 52

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

    Small variant calling for haploid samples

    Python 62 22

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

    Nextflow 181 88

  6. fastcat fastcat Public

    Ultra fast FASTQ and BAM processing, filtering, concatenation and sequencing QC/statistics.

    C 59 4

Repositories

Showing 10 of 28 repositories
  • fastcat Public

    Ultra fast FASTQ and BAM processing, filtering, concatenation and sequencing QC/statistics.

    epi2me-labs/fastcat's past year of commit activity
    C 59 4 0 0 Updated Sep 26, 2026
  • wf-aav-qc Public
    epi2me-labs/wf-aav-qc's past year of commit activity
    Python 8 11 2 0 Updated Sep 17, 2026
  • epi2me-labs/wf-transcriptomes's past year of commit activity
    Python 116 51 23 0 Updated Aug 5, 2026
  • wf-template Public

    Nextflow workflow template repository

    epi2me-labs/wf-template's past year of commit activity
    Python 20 36 0 0 Updated Jul 29, 2026
  • epi2me-labs/wf-human-variation's past year of commit activity
    Nextflow 181 88 27 2 Updated Jul 20, 2026
  • wf-flu Public
    epi2me-labs/wf-flu's past year of commit activity
    Python 22 9 4 0 Updated Jun 1, 2026
  • epi2me-labs/wf-basecalling's past year of commit activity
    Nextflow 52 30 13 2 Updated Apr 10, 2026
  • ezcharts Public
    epi2me-labs/ezcharts's past year of commit activity
    Python 23 0 0 0 Updated Mar 27, 2026
  • wf-amplicon Public
    epi2me-labs/wf-amplicon's past year of commit activity
    Python 46 14 3 0 Updated Mar 13, 2026
  • wf-alignment Public
    epi2me-labs/wf-alignment's past year of commit activity
    Python 35 27 3 0 Updated Mar 9, 2026

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