badread

{
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    "numpy",
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  "deprecation_reason": null,
  "desc": "Long read simulator that can imitate many types of read problems",
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  "enrichment_fetched_at": "2026-06-20T23:35:44+00:00",
  "first_seen": "2026-06-20T23:34:18+00:00",
  "full_name": "badread",
  "github_default_branch": "main",
  "github_last_commit_at": "2026-04-22T06:46:21Z",
  "github_readme_excerpt": "\u003cp align=\"center\"\u003e\u003cpicture\u003e\u003csource srcset=\"images/logo-dark.png\" media=\"(prefers-color-scheme: dark)\"\u003e\u003cimg src=\"images/logo.png\" alt=\"Badread\" width=\"75%\"\u003e\u003c/picture\u003e\u003c/p\u003e\n\nBadread is a long-read simulator tool that makes \u2013 you guessed it \u2013 bad reads! It can imitate many kinds of problems one might encounter in real long-read sets: chimeras, low-quality regions, systematic basecalling errors and more.\n\nBadread does not try to be best at imitating real reads (though it\u0027s not too bad, see [this comparison between Badread and other long-read simulators](comparison)). Rather, it was intended to give users _control_ over the quality of its simulated reads. I made Badread for the purpose of testing tools which take long reads as input. With it, one can increase the rate of different types of read problems, to see what effect it has.\n\nBadread is published in the [Journal of Open Source Software](http://joss.theoj.org). If you use it in your research, please cite this manuscript:\u003cbr\u003e\n\u003e Wick RR. Badread: simulation of error-prone long reads. _Journal of Open Source Software_. 2019;4(36):1316. doi:[10.21105/joss.01316](https://doi.org/10.21105/joss.01316).\n\n[![Coverage Status](https://coveralls.io/repos/github/rrwick/Badread/badge.svg?branch=master\u0026service=github)](https://coveralls.io/github/rrwick/Badread?branch=master) [![License GPL v3](https://img.shields.io/badge/license-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html) [![status](http://joss.theoj.org/papers/a9ae38312391668801949ddc59e10cb1/status.svg)](http://joss.theoj.org/papers/a9ae38312391668801949ddc59e10cb1) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2622997.svg)](https://doi.org/10.5281/zenodo.2622997)\n\n\n## Table of contents\n\n- [Table of contents](#table-of-contents)\n- [Requirements](#requirements)\n- [Installation](#installation)\n  - [Install from source](#install-from-source)\n  - [Run without installation](#run-without-installation)\n- [Quick usage](#quick-usage)\n- [Method](#method)\n- [De",
  "github_repo": "rrwick/Badread",
  "github_stars": 290,
  "github_topics": [],
  "homepage": "https://github.com/rrwick/Badread",
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  "installs_30d": 35,
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  "last_seen": "2026-06-20T23:34:18+00:00",
  "license": "GPL-3.0-or-later",
  "llm_generated_at": null,
  "llm_model": null,
  "name": "badread",
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  "rank_30d": 5439,
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  "raw_hash": "4d7c756c5b9ebb31",
  "recommended_dependencies": [],
  "revision": 0,
  "ruby_source_path": "Formula/b/badread.rb",
  "tap": "homebrew/core",
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  "version_stable": "0.4.2",
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}