{"id":25596875,"url":"https://github.com/nanoporetech/minimappy","last_synced_at":"2025-08-05T08:15:13.877Z","repository":{"id":85586435,"uuid":"100385183","full_name":"nanoporetech/minimappy","owner":"nanoporetech","description":"Python bindings to minimap2","archived":false,"fork":false,"pushed_at":"2017-09-18T09:46:55.000Z","size":1510,"stargazers_count":16,"open_issues_count":0,"forks_count":1,"subscribers_count":12,"default_branch":"master","last_synced_at":"2025-04-13T02:32:58.480Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nanoporetech.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-08-15T14:21:49.000Z","updated_at":"2022-05-18T23:51:03.000Z","dependencies_parsed_at":"2023-03-13T05:57:06.873Z","dependency_job_id":null,"html_url":"https://github.com/nanoporetech/minimappy","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/nanoporetech/minimappy","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Fminimappy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Fminimappy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Fminimappy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Fminimappy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nanoporetech","download_url":"https://codeload.github.com/nanoporetech/minimappy/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Fminimappy/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":268859123,"owners_count":24318874,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-08-05T02:00:12.334Z","response_time":2576,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-02-21T12:35:00.007Z","updated_at":"2025-08-05T08:15:13.844Z","avatar_url":"https://github.com/nanoporetech.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"minimappy\n=========\n\nStatus\n------\n\nSince the time of writing Heng Li, the author of minimap2, has provided a\npython binding in the minimap2 source and at https://pypi.python.org/pypi/mappy.\nUsers are strongly encouraged to use Heng's python library rather that\nthe version presented here. Despite its short life, the latter will be no\nlonger supported out of deference to Heng's version.\n\n\n[![Build Status](https://travis-ci.org/nanoporetech/minimappy.svg?branch=master)](https://travis-ci.org/nanoporetech/minimappy)\n\nPython bindings to `minimap2` aligner; sufficient to load and index and perform\nalignments of sequences to the index to obtain basic statistics.\n\nThese python bindings are licensed under Mozilla Public License 2.0, minimap is\nlicenced The MIT License.\n\nDocumentation can be found at https://nanoporetech.github.io/minimappy/.\n\nInstallation\n------------\n\nThe git source repository contains minimap2 as a submodule. The repository\nshould therefore be cloned using the recursive option.\n\nThe package `setup.py` script requires `libminimap2.a` to have been built in the\nsubmodule directory before running. This can be performed via the `libminimap2.a`\ntarget. To build and install the package one should\ntherefore run:\n\n    git clone --recursive https://github.com/nanoporetech/minimappy.git\n    make minimap2/libminimap2.a \n    python setup.py install\n\n\nPerforming Alignments\n---------------------\n\nThe `MinimapAligner` class provides a pythonic interface to `minimap2` aligner.\nIt takes as input a minimap index or .fasta reference on construction and can\nthen be used to find alignments of sequences given as strings:\n\n```python\nfrom minimappy import MinimapAligner\nindex = 'path/to/index' # the path given to minimap2 index\nseq = 'ACGATCGCGATCGA'\n\naligner = MinimapAligner(index)\nalignments = aligner.align_seq(seq)\nprint('Found {} alignments.'.format(len(alignments))\nfor aln in alignments:\n    print('  ', aln)\n```\n\nThe alignments are returned as a named tuple, e.g.:\n\n```python\nAlignment(rname='yeast', orient='+', pos=0, mapq=60, cigar='915M3D29M3D27M3D13M', NM=12, flags=0)\n```\n\nAlignment parameters can be given as they are on the `minimap2` command line:\n\n```python\nfrom minimappy import MinimapAligner\nindex = 'path/to/index'\noptions = '-ax map10k'\naligner = MinimapAligner(index, options=options)\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnanoporetech%2Fminimappy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnanoporetech%2Fminimappy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnanoporetech%2Fminimappy/lists"}