{"id":13510023,"url":"https://github.com/FelixKrueger/Bismark","last_synced_at":"2025-03-30T15:30:36.611Z","repository":{"id":37088853,"uuid":"45748259","full_name":"FelixKrueger/Bismark","owner":"FelixKrueger","description":"A tool to map bisulfite converted sequence reads and determine cytosine methylation states","archived":false,"fork":false,"pushed_at":"2025-01-06T07:26:59.000Z","size":39962,"stargazers_count":402,"open_issues_count":28,"forks_count":104,"subscribers_count":14,"default_branch":"master","last_synced_at":"2025-01-06T08:29:05.016Z","etag":null,"topics":["bioinformatics","dna","methylation"],"latest_commit_sha":null,"homepage":"http://felixkrueger.github.io/Bismark/","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/FelixKrueger.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"license.txt","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":"2015-11-07T18:14:13.000Z","updated_at":"2025-01-06T07:26:27.000Z","dependencies_parsed_at":"2024-03-27T21:31:26.884Z","dependency_job_id":"be9e9ef9-fbe3-4010-9a6d-666942c497e0","html_url":"https://github.com/FelixKrueger/Bismark","commit_stats":{"total_commits":832,"total_committers":19,"mean_commits":43.78947368421053,"dds":"0.13461538461538458","last_synced_commit":"acf965cdf9e0a2814f09c087811683c1651c36c1"},"previous_names":[],"tags_count":64,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FelixKrueger%2FBismark","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FelixKrueger%2FBismark/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FelixKrueger%2FBismark/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FelixKrueger%2FBismark/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/FelixKrueger","download_url":"https://codeload.github.com/FelixKrueger/Bismark/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246338595,"owners_count":20761405,"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":["bioinformatics","dna","methylation"],"created_at":"2024-08-01T02:01:21.444Z","updated_at":"2025-03-30T15:30:31.599Z","avatar_url":"https://github.com/FelixKrueger.png","language":"HTML","funding_links":[],"categories":["HTML","bioinformatics"],"sub_categories":[],"readme":"# Bismark\n\n[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bismark/README.html)\n\n\u003e **See the documentation**: \u003chttps://felixkrueger.github.io/Bismark\u003e\n\nBismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as [SeqMonk](http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), and enables a researcher to analyse the methylation levels of their samples straight away. It's main features are:\n\n- Bisulfite mapping and methylation calling in one single step\n- Supports single-end and paired-end read alignments\n- Supports ungapped, gapped or spliced alignments\n- Alignment seed length, number of mismatches etc. are adjustable\n- Output discriminates between cytosine methylation in `CpG`, `CHG` and `CHH` context\n\n## Documentation\n\nThe Bismark documentation can be found with the code in the [docs](docs) subfolder and can also be read online: \u003chttps://felixkrueger.github.io/Bismark/\u003e\n\nThere is also an overview of the alignment modes that are currently supported by Bismark: [Bismark alignment modes](http://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_alignment_modes.pdf) (pdf).\n\n## Installation\n\nBismark is written in Perl and is executed from the command line. To install Bismark simply download the latest release of the code from the [Releases page](https://github.com/FelixKrueger/Bismark/releases) and extract the files into a Bismark installation folder.\n\nBismark needs the following tools to be installed and ideally available in the `PATH` environment:\n\n- [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/) or [HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml) or [minimap2](https://lh3.github.io/minimap2/minimap2.html)\n- [Samtools](http://www.htslib.org/)\n\n## Links\n\n- Bismark Publication\n  - http://www.ncbi.nlm.nih.gov/pubmed/21493656\n- Our review about primary data analysis in BS-Seq\n  - http://www.ncbi.nlm.nih.gov/pubmed/22290186\n  \n## Credits\n\nBismark was written by Felix Krueger, part of the [Babraham Bioinformatics](http://www.bioinformatics.babraham.ac.uk/projects/bismark/) group.\n\n## Licences\n\nBismark itself is free software, `bismark2report` and `bismark2summary` produce HTML graphs powered by [Plot.ly](https://plot.ly/javascript/) which are also free to use and look at!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FFelixKrueger%2FBismark","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FFelixKrueger%2FBismark","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FFelixKrueger%2FBismark/lists"}