Bin Oxford Nanopore reads by cumulative sequencing time intervals, using the read start time that MinKNOW, Guppy and Dorado embed in every FASTQ header. Useful to answer "how long did I actually need to sequence?" — for time-to-detection studies, assembly saturation curves, or benchmarking real-time pipelines.
fastq_pass/ ──► sample_0-1h_125437reads_1103093674bp.fastq.gz
sample_0-2h_225891reads_2087456221bp.fastq.gz (bins are cumulative)
sample_0-3h_301255reads_2812345678bp.fastq.gz
Compatible with Guppy/MinKNOW (start_time=) and Dorado (st:Z:) headers. Fast
(each read compressed once, ~100× faster than v0.1), low-memory (streaming), parallel, and
pure standard library.
Install
pip install nanotimesort
Requires Python ≥ 3.8. No other dependencies.
Usage
nanotimesort -f /path/to/fastq_pass/ -o /path/to/output/ -i 1h -p my_sample
📖 Full documentation — CLI reference, tutorial with example data, header compatibility, design notes and FAQ — is in the wiki.
Citation
If you use nanoTimeSort in your research, please cite it. GitHub's "Cite this repository"
button (from CITATION.cff) gives APA/BibTeX entries, and the DOI badge above
resolves to the citable Zenodo archive of the latest release.
License
MIT © Marc-Olivier Duceppe
1 maintainer
Metadata
1 maintainer
Release files for nanotimesort 1.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| nanotimesort-1.1.0.tar.gz | 16.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| nanotimesort-1.1.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 28.1 kB
Release files / nanotimesort-1.1.0.tar.gz
| Download URL | nanotimesort-1.1.0.tar.gz |
|---|---|
| Size | 16.0 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
e844bf8d5d926ac8c19c628b92ee3e459ae9f774c0134f692a3052f7c17bc8a4
|
|
BLAKE2b-256 checksum How to use checksums |
add91dd924d4340ffb8d71e9084196c5fcfdd38412419438793b7e60eb2ce859
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 7, 2026.
Transparency logRelease files / nanotimesort-1.1.0-py3-none-any.whl
| Download URL | nanotimesort-1.1.0-py3-none-any.whl |
|---|---|
| Size | 12.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
6737a69823ada282e21249ee1db4ffc8608ca8e3d42bfb302ce9a2eb48446e0d
|
|
BLAKE2b-256 checksum How to use checksums |
141676ac824cf6af1a1e6154c243107d898dad7f679e5c3dedbf37c70f81a563
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 7, 2026.
Transparency log
