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@rnajena

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JannesSP/README.md

Jannes Spangenberg

Scientific Software Engineer • Data Scientist • Bioinformatics PhD
Building production-minded open-source tooling for sequencing data, signal processing, and reproducible research software.

LinkedIn XING

What I build

I develop software for noisy, high-volume biological data with a focus on:

  • Python and C++ tooling for real-world sequencing workflows
  • signal processing, AI, DNNs, HMMs, benchmarking, and model validation
  • maintainable packaging, testing, documentation, and reproducible delivery
  • turning research-grade methods into software other people can install and use

Featured repositories

Dynamont

A segmentation and resquiggling tool for Oxford Nanopore raw signals, combining dynamic programming, HMM-style modeling, C++ performance, Python packaging, tested models, and documented CLI workflows.

Highlights: C++/Python codebase, PyPI and Conda distribution, DOI/CITATION metadata, releases, tests, and reusable default pore models.

Dynamont repo card

Read5

A unified Python wrapper for reading FAST5, SLOW5, BLOW5, and POD5 files through one consistent interface, with documentation, packaging, tests, and practical usability for nanopore analysis workflows.

Highlights: multi-format abstraction, PyPI and Conda packaging, full docs, releases, DOI/CITATION metadata, and production-style library design.

Read5 repo card

GitHub activity

GitHub stats GitHub streak

If you are hiring for data science, machine learning, or scientific software roles, the best examples of how I work are Dynamont and Read5.

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  1. read5.github.io read5.github.io Public

    Documentation for the https://github.com/JannesSP/read5 repository

    HTML

  2. rnajena/read5 rnajena/read5 Public

    Wrapper to read fast5, slow5, blow5 and pod5 files.

    Python 13 1

  3. rnajena/magnipore rnajena/magnipore Public

    Magnipore: Differential single nucleotide changes of ONT signals

    Red 6

  4. rnajena/read5_ont rnajena/read5_ont Public

    Wrapper to read fast5 and pod5 files.

    Python 2 1