awesome-nanopore
github.com/goekelab/awesome-nanopore ↗A curated list of awesome nanopore analysis tools.
Use this list with your AI agent
Add the Context Awesome MCP server to Claude, Cursor, or any MCP client, then ask:
"Show me assembly resources from awesome-nanopore"
Installation instructions →What's inside
Software packages
- AutocyclerAssembly
[Rust] -
- bambuTranscriptomics
[R] -
- BLAZETranscriptomics
[Python] -
- BonitoBasecalling
[Python] - A PyTorch Basecaller for Oxford Nanopore Reads (research, not production basecaller)
- CausalcallBasecalling
[Python] -
- ChironBasecalling
[Python] -
Pipelines
- bambu-pipe
[Nextflow] -
- MOP2
[Nextflow] -
- nf-core/nanoseq
[Nextflow] -
- nf-WochenendeMetagenomics
modular and flexible alignment-based shotgun metagenome analysis
Deprecated / superseded
- mAFiA
[Python] -
- Megalodon
[C++] - Research modified base caller which uses rerio, remora and a genome (deprecated by ONT 2023 for Dorado).
- modbam2bed
[C++] - Convert modified base calls from megalodon etc to bedMethyl format (deprecated by ONT 2023 for Modkit)
- tombo detect_modifications
[Python] -
- tombo resquiggle
deprecated by ONT 2023, only compatible with RNA002 dRNA-seq chemistry & R9.4.1 chemistry)
Showing a sample of 86 resources. View the full list on GitHub →