2 Bioinformatic Resources

Comprehensive list of bioinformatic tools and resources for working with Oxford Nanopore sequencing data.

2.1 Bioinformatic tools

dorado
Official basecalling software for processing ONT data.
Docs: https://software-docs.nanoporetech.com/dorado/latest/
GitHub: https://github.com/nanoporetech/dorado

modkit
Official toolkit for processing and analyzing base modifications from ONT data.
Docs: https://nanoporetech.github.io/modkit/
GitHub: https://github.com/nanoporetech/modkit

pod5
Official Python toolkit for processing ONT raw signal data.
Docs: https://software-docs.nanoporetech.com/pod5/latest/
GitHub: https://github.com/nanoporetech/pod5-file-format

minimod
Toolkit for working with base modifications. This is an alternative to modkit that is about 20× faster.
Docs: https://warp9seq.github.io/minimod/
GitHub: https://github.com/warp9seq/minimod
Paper: https://www.biorxiv.org/content/10.1101/2025.07.16.665072v1

slow5tools
Toolkit for compressing legacy FAST5 and POD5 file formats (supports lossless and lossy POD5 compression).
Docs: https://hasindu2008.github.io/slow5tools/
GitHub: https://github.com/hasindu2008/slow5tools
Paper: https://pmc.ncbi.nlm.nih.gov/articles/PMC12212073/

minimap2
Sequence aligner for long-read sequence data.
GitHub: https://github.com/lh3/minimap2
Paper: https://academic.oup.com/bioinformatics/article/34/18/3094/4994778

2.2 Pipelines

wf-transcriptomes
Nextflow-based pipeline from epi2me-labs for long-read transcriptome analysis (cDNA or direct RNA). Performs alignment, transcript assembly, annotation, quantification, and optional differential expression/usage analysis.
GitHub: https://github.com/epi2me-labs/wf-transcriptomes

nf-core/nanoseq
Nextflow-based pipeline from nf-core for nanopore sequence data. Performs demultiplexing, QC and alignment.
GitHub: https://github.com/nf-core/nanoseq