{"id":17174995,"url":"https://github.com/tobiasrausch/alfred","last_synced_at":"2026-02-26T11:23:30.430Z","repository":{"id":5588400,"uuid":"52509133","full_name":"tobiasrausch/alfred","owner":"tobiasrausch","description":"BAM Statistics, Feature Counting and Annotation","archived":false,"fork":false,"pushed_at":"2025-02-17T16:42:57.000Z","size":22914,"stargazers_count":147,"open_issues_count":4,"forks_count":12,"subscribers_count":9,"default_branch":"main","last_synced_at":"2025-03-29T04:05:09.787Z","etag":null,"topics":["alfred","alignment-metrics","coverage-distribution","feature-counting","insert-size","quality","quality-control","read-counts","sequencing"],"latest_commit_sha":null,"homepage":"https://www.gear-genomics.com/alfred/","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/tobiasrausch.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-02-25T08:32:15.000Z","updated_at":"2025-03-23T17:44:08.000Z","dependencies_parsed_at":"2024-01-10T09:40:14.883Z","dependency_job_id":"af956520-5fba-46a2-bb99-4d892fee9392","html_url":"https://github.com/tobiasrausch/alfred","commit_stats":{"total_commits":678,"total_committers":3,"mean_commits":226.0,"dds":"0.23303834808259583","last_synced_commit":"9b5cd275638a4f0236409de053ab22b0d2cfb6a4"},"previous_names":[],"tags_count":27,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2Falfred","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2Falfred/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2Falfred/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2Falfred/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tobiasrausch","download_url":"https://codeload.github.com/tobiasrausch/alfred/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247289424,"owners_count":20914464,"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","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":["alfred","alignment-metrics","coverage-distribution","feature-counting","insert-size","quality","quality-control","read-counts","sequencing"],"created_at":"2024-10-14T23:55:27.598Z","updated_at":"2026-02-26T11:23:30.383Z","avatar_url":"https://github.com/tobiasrausch.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cp align=\"center\"\u003e\n   \u003cimg width=\"450\" src=\"https://raw.githubusercontent.com/tobiasrausch/alfred/master/alfred.png\"\u003e\n   \u003ch1\u003e\u003c/h1\u003e\n\u003c/p\u003e\n\n[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/alfred/README.html)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/alfred/badges/downloads.svg)](https://anaconda.org/bioconda/alfred)\n[![C/C++ CI](https://github.com/tobiasrausch/alfred/workflows/C/C++%20CI/badge.svg)](https://github.com/tobiasrausch/alfred/actions)\n[![Docker CI](https://github.com/tobiasrausch/alfred/workflows/Docker%20CI/badge.svg)](https://hub.docker.com/r/trausch/alfred/)\n[![GitHub license](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://github.com/tobiasrausch/alfred/blob/master/LICENSE)\n[![GitHub Releases](https://img.shields.io/github/release/tobiasrausch/alfred.svg)](https://github.com/tobiasrausch/alfred/releases)\n\n## Alfred: BAM alignment statistics, feature counting and feature annotation\n\nAlfred is available as a [Bioconda package](https://anaconda.org/bioconda/alfred), as a pre-compiled statically linked binary from [Alfred's github release page](https://github.com/tobiasrausch/alfred/releases/), as a singularity container [SIF file](https://github.com/tobiasrausch/alfred/releases/) or as a minimal [Docker container](https://hub.docker.com/r/trausch/alfred/). Please have a look at [Alfred's documentation](https://www.gear-genomics.com/docs/alfred/) for any installation or usage questions.\n\n[Source Code](https://github.com/tobiasrausch/alfred/)\n\n[Web Application](https://www.gear-genomics.com/alfred/)\n\n[Documentation](https://www.gear-genomics.com/docs/alfred/)\n\n## Citation\n\nTobias Rausch, Markus Hsi-Yang Fritz, Jan O Korbel, Vladimir Benes.      \nAlfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing.\nBioinformatics. 2019 Jul 15;35(14):2489-2491.\n[https://doi.org/10.1093/bioinformatics/bty1007](https://doi.org/10.1093/bioinformatics/bty1007)\n\n\nLicense\n-------\nAlfred is distributed under the BSD 3-Clause license. Consult the accompanying [LICENSE](https://github.com/tobiasrausch/alfred/blob/master/LICENSE) file for more details.\n\n## Credits\n\n[HTSlib](https://github.com/samtools/htslib) is heavily used for all alignment and VCF/BCF processing. [Boost](https://www.boost.org/) for various data structures and algorithms and [Edlib](https://github.com/Martinsos/edlib) for pairwise alignments using edit distance.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftobiasrausch%2Falfred","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftobiasrausch%2Falfred","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftobiasrausch%2Falfred/lists"}