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awesome-nanopore

Awesome

List of software packages for Nanopore sequencing data analysis, including basecalling, DNA/RNA modifications, etc. Contributions welcome...

Software packages

Basecalling

Adaptive sampling / ReadUntil Real-time mapping / signal mapping

Segmentation

DNA modification analysis

RNA modification analysis

RNA structure prediction

Poly(A) tail length estimation

Transcript discovery and quantification

Raw signal data manipulation, conversion, visualisation, etc.

Genome Assembly

  • Flye - [C++] - Single molecule sequence assembler with good polishing capabilities
  • Shasta - [C] - Very fast and capable nanopore assembler

Single-cell analysis

Pipelines

Metagenomics

Reads simulation

Contributing

We welcome contributions and suggestions! Please follow the steps below to contribute:

  1. Fork this repository
  2. Make a change to README.md in this format: [RESOURCE](LINK) - [language(s)] - DESCRIPTION
  3. Submit a pull request.

Citation

Wan, Y.K., Hendra, C., Pratanwanich, P.N. & Göke, J. Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data. Trends in Genetics (2021). https://doi.org/10.1016/j.tig.2021.09.001.

What is an awesome list?

According to the official awesome Github repository, an awesome list on GitHub is "a curation of actual awesome stuff", so an awesome list only includes items that has been researched by a contributor who would personally recommend the items. To learn more, please read the official awesome manifesto.

Contact

This repository was created by Yuk Kei Wan.