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 git+https://github.com/duceppemo/nanoTimeSort.git
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.
License
MIT © Marc-Olivier Duceppe
1 maintainer
Metadata
1 maintainer
Release files for nanotimesort 1.0.0
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