flye

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    "python@3.14",
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  "desc": "De novo assembler for single molecule sequencing reads using repeat graphs",
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  "enrichment_fetched_at": "2026-06-20T23:37:44+00:00",
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  "full_name": "flye",
  "github_default_branch": "flye",
  "github_last_commit_at": "2026-04-03T20:56:14Z",
  "github_readme_excerpt": "Flye assembler\n==============\n\n[![BioConda Install](https://img.shields.io/conda/dn/bioconda/flye.svg?style=flag\u0026label=BioConda%20install)](https://anaconda.org/bioconda/flye)\n\n### Version: 2.9.6\n\nFlye is a de novo assembler for single-molecule sequencing reads,\nsuch as those produced by PacBio and Oxford Nanopore Technologies.\nIt is designed for a wide range of datasets, from small bacterial projects\nto large mammalian-scale assemblies. The package represents a complete\npipeline: it takes raw PacBio / ONT reads as input and outputs polished contigs.\nFlye also has a special mode for metagenome assembly.\n\nCurrently, Flye will produce collapsed assemblies of diploid genomes, \nrepresented by a single mosaic haplotype. To recover two phased haplotypes\nconsider applying [HapDup](https://github.com/fenderglass/hapdup) after the assembly.\n\nIf you are using Flye / metaFlye to assemble heteroztgous bacterial genomes or metagenomes,\nyou may consider using [strainy](https://github.com/katerinakazantseva/strainy) to\ncall and quanitify heterozygosity and reveal collapsed strains.\n\nManuals\n-------\n\n- [Installation instructions](docs/INSTALL.md)\n- [Usage](docs/USAGE.md)\n- [FAQ](docs/FAQ.md)\n\nLatest updates\n--------------\n\nFlye 2.9.6 release (2 May 2025)\n==============================\n* Minor fix release, most assmeblies should not change\n* Fixed rare race condition in polishing stage\n* R10 ONT parameters (3% error) are now default for --nano-hq\n\nFlye 2.9.5 release (27 Aug 2024)\n===============================\n* Python 3.12 support, Python 2 dropped\n\nFlye 2.9.4 release (14 May 2024)\n===============================\n* Minor technical changes\n\n\n### Flye 2.9.3 release (28 November 2023)\n* Disjointig step speedup for `--nano-hq` mode\n* Improved `--keep-haplotypes` mode preserves more heterozygous SVs\n* A few bug fixes\n\n\n### Flye 2.9.2 release (18 March 2023)\n* Update to minimap 2.24 + using HiFi and Kit14 parameters for faster alignment\n* Fixed a few small bugs and corner cases\n* Polish",
  "github_repo": "mikolmogorov/Flye",
  "github_stars": 939,
  "github_topics": [],
  "homepage": "https://github.com/mikolmogorov/Flye",
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  "last_seen": "2026-06-20T23:34:18+00:00",
  "license": "BSD-3-Clause AND Apache-2.0 AND BSL-1.0 AND CC-BY-3.0 AND MIT",
  "llm_generated_at": null,
  "llm_model": null,
  "name": "flye",
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  "rank_30d": 8009,
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  "raw_hash": "6a4d3dc29b0d1644",
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  "revision": 0,
  "ruby_source_path": "Formula/f/flye.rb",
  "tap": "homebrew/core",
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  "version_head": "HEAD",
  "version_stable": "2.9.6",
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  "why_use_this": null
}