{"id":36092170,"url":"https://github.com/smithlabcode/methpipe","last_synced_at":"2026-01-10T20:00:06.944Z","repository":{"id":16229425,"uuid":"18976885","full_name":"smithlabcode/methpipe","owner":"smithlabcode","description":"A pipeline for analyzing DNA methylation data from bisulfite sequencing.","archived":true,"fork":false,"pushed_at":"2022-10-07T20:37:20.000Z","size":9744,"stargazers_count":70,"open_issues_count":0,"forks_count":27,"subscribers_count":16,"default_branch":"master","last_synced_at":"2025-04-01T00:29:55.441Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://smithlabresearch.org/methpipe","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/smithlabcode.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-04-21T00:12:54.000Z","updated_at":"2025-01-31T19:46:54.000Z","dependencies_parsed_at":"2023-01-11T20:24:42.591Z","dependency_job_id":null,"html_url":"https://github.com/smithlabcode/methpipe","commit_stats":null,"previous_names":[],"tags_count":16,"template":false,"template_full_name":null,"purl":"pkg:github/smithlabcode/methpipe","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fmethpipe","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fmethpipe/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fmethpipe/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fmethpipe/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/smithlabcode","download_url":"https://codeload.github.com/smithlabcode/methpipe/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fmethpipe/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28257658,"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":"2026-01-10T02:00:06.867Z","response_time":57,"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":"2026-01-10T20:00:05.824Z","updated_at":"2026-01-10T20:00:06.920Z","avatar_url":"https://github.com/smithlabcode.png","language":"C++","readme":"NOTICE: MethPipe is no longer maintained in this repository\n============================================================\n\nMethPipe is now [DNMTools](https://github.com/smithlabcode/dnmtools). The\nMethPipe repository will remain open for issues and discussion, but further releases,\nupdates and fixes will no longer be maintained in this page. We strongly\nrecommend that users replace their existing release of MethPipe with the\nmost recent version of DNMTools, which contains all existing MethPipe programs\nalong with various fixes, improvements and novel programs for bisulfite sequencing\ndata analysis.\n\n[Visit the DNMTools repository](https://github.com/smithlabcode/dnmtools)\n\n------------------------------------------------------------------\n\nThe MethPipe software package is a computational pipeline for\nanalyzing bisulfite sequencing data (WGBS and RRBS). MethPipe provides\ntools methylation-specific technical evaluation of sequencing data,\nand for estimating methylation levels at individual cytosines.\nAdditionally, MethPipe includes tools for identifying higher-level\nmethylation features, such as hypo-methylated regions (HMR), partially\nmethylated domains (PMD), hyper-methylated regions (HyperMR), and\nallele-specific methylated regions (AMR).\n\nRelease 5.0.1\n===================\n\nThis new release no longer supports `mr` files, which means that the\n`to-mr` program has been eliminated and replaced by a program called\n`format_reads`, which merges mates in paired-end SAM files, also\nconverting them to a standardized SAM format depending on the mapper\nit originates from.  Additionally, the `htslib` library is now\nrequired, and instructions to install it in different environments are\ndiscussed below.\n\nIf working with MR files is necessary for your analysis, we refer\nusers to methpipe version [5.0.1](https://github.com/smithlabcode/methpipe/releases/tag/v5.0.1),\nwhich is the last release that contains programs that take MR as\ninput.\n\n## Installing release 5.0.1\n\n### Required libraries\n\n* A recent compiler: most users will be building and installing this\n  software with GCC. We require a compiler that fully supports C++11,\n  so we recommend using at least GCC 5.8. There are still many systems\n  that install a very old version of GCC by default, so if you have\n  problems with building this software, that might be the first thing\n  to check.\n* The GNU Scientific Library: this has always been required. It can be\n  installed using `apt` on Linux, using `brew` on macOS, or from\n  source available [here](http://www.gnu.org/software/gsl).\n* The Zlib compression library. Most likely you already have this\n  installed on your system. If not, it can be installed using `apt`\n  on Linux through the package `zlib1g-dev`. On macOS, Zlib can be\n  installed with `brew`.\n* The HTSlib library, which can be installed through `brew`\n  on macOS, through `apt` on Linux, or from source downloadable\n  [here](https://github.com/samtools/htslib).\n\n### Configuration\n\n1. Download methpipe-5.0.1.tar.gz [here](https://github.com/smithlabcode/methpipe/releases/download/v5.0.1/methpipe-5.0.1.tar.gz).\n2. Unpack the archive:\n```\n$ tar -zxvf methpipe-5.0.1.tar.gz\n```\n3. Move into the methpipe directory and create a build directory:\n```\n$ cd methpipe-5.0.1\n$ mkdir build \u0026\u0026 cd build\n```\n4. Run the configuration script:\n```\n$ ../configure\n```\nIf you do not want to install the methpipe system-wide, or if you do\nnot have admin privileges, specify a prefix directory:\n```\n$ ../configure --prefix=/some/reasonable/place\n```\nIf you installed HTSlib yourself in some non-standard directory,\nyou must specify the location like this:\n```\n$ ../configure CPPFLAGS='-I /path/to/htslib/headers' \\\n               LDFLAGS='-L/path/to/htslib/lib'\n```\n\n### Building and installing the tools\n\nIf you are still in the `build` directory, run `make` to compile the\ntools, and then `make install` to install them. If your HTSlib is not\ninstalled system-wide, then you might need to udpate your library\npath:\n```\n$ export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/path/to/htslib/lib\n```\n\n### Building and installing from source\n\nWe strongly recommend using methpipe through the latest stable release\nunder the releases section on GitHub. However, developers who wish to\nwork on the latest commits, which are potentially unstable, can\ncompile the cloned repository using the `Makefile` available in the\nrepository. If HTSLib is available system-wide, compile by running\n```\nmake\n```\n\nUsage\n=====\n\nRead methpipe-manual.pdf in the docs directory.\n\nContacts and bug reports\n========================\n\nAndrew D. Smith\nandrewds@usc.edu\n\nBen Decato\ndecato@usc.edu\n\nMeng Zhou\nmengzhou@usc.edu\n\nMethPipe and MethBase Users' Mailinglist\nmethpipe@googlegroups.com\nhttp://groups.google.com/group/methpipe\n\nCopyright and License Information\n=================================\n\nCopyright (C) 2018-2021\nUniversity of Southern California,\nAndrew D. Smith\n\nCurrent Authors: Andrew D. Smith, Ben Decato, Meng Zhou, Liz Ji,\nTerence Li, Guilherme de Sena Brandine\n\nThis is free software: you can redistribute it and/or modify it under\nthe terms of the GNU General Public License as published by the Free\nSoftware Foundation, either version 3 of the License, or (at your\noption) any later version.\n\nThis software is distributed in the hope that it will be useful, but\nWITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU\nGeneral Public License for more details.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithlabcode%2Fmethpipe","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsmithlabcode%2Fmethpipe","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithlabcode%2Fmethpipe/lists"}