https://github.com/lgautier/fastq-and-furious

Efficient handling of FASTQ files from Python
https://github.com/lgautier/fastq-and-furious

fastq ngs python

Last synced: 7 months ago
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Efficient handling of FASTQ files from Python

• Host: GitHub
• URL: https://github.com/lgautier/fastq-and-furious
• Owner: lgautier
• License: mit
• Created: 2017-01-29T18:27:38.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2024-09-03T21:47:57.000Z (about 1 year ago)
• Last Synced: 2025-02-13T21:14:00.249Z (8 months ago)
• Topics: fastq, ngs, python
• Language: Python
• Homepage: https://lgautier.github.io/fastq-and-furious/
• Size: 2.56 MB
• Stars: 51
• Watchers: 2
• Forks: 5
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# fastq-and-furious

(... because it turned out that the performance bottleneck for an

[algorithm-focused implementation of bottom-sketches (MinHash sketches)](https://github.com/lgautier/mashing-pumpkins)

was the parsing of FASTQ files).

Project web page: [https://lgautier.github.io/fastq-and-furious/](https://lgautier.github.io/fastq-and-furious/)

[![Python package](https://github.com/lgautier/fastq-and-furious/actions/workflows/pythonpackage.yml/badge.svg)](https://github.com/lgautier/fastq-and-furious/actions/workflows/pythonpackage.yml)

[![Pypi release](https://img.shields.io/pypi/v/fastq-and-furious.svg)](https://img.shields.io/pypi/v/fastq-and-furious.svg)

Efficient and flexible parsing of FASTQ files(*) from Python. It is about as fast as the fastest parser with C extensions, but it is substantially more flexible.