{"id":22621083,"url":"https://github.com/pdimens/lepwrap","last_synced_at":"2025-09-20T07:53:29.638Z","repository":{"id":43676112,"uuid":"260516189","full_name":"pdimens/LepWrap","owner":"pdimens","description":"A pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring and orienting genome assemblies with said linkage maps.","archived":false,"fork":false,"pushed_at":"2025-06-24T19:28:31.000Z","size":10216,"stargazers_count":13,"open_issues_count":1,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-06-24T20:32:20.463Z","etag":null,"topics":["bioinformatics","genome-assembly","linkage","linkage-mapping","snakemake"],"latest_commit_sha":null,"homepage":"https://github.com/pdimens/LepWrap/wiki","language":"Perl","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/pdimens.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-05-01T17:18:28.000Z","updated_at":"2025-06-24T19:25:45.000Z","dependencies_parsed_at":"2024-12-08T22:27:48.806Z","dependency_job_id":null,"html_url":"https://github.com/pdimens/LepWrap","commit_stats":{"total_commits":650,"total_committers":1,"mean_commits":650.0,"dds":0.0,"last_synced_commit":"d466ad177d1f21457fe689a4d5f9071516e35aca"},"previous_names":[],"tags_count":16,"template":false,"template_full_name":null,"purl":"pkg:github/pdimens/LepWrap","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2FLepWrap","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2FLepWrap/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2FLepWrap/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2FLepWrap/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pdimens","download_url":"https://codeload.github.com/pdimens/LepWrap/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2FLepWrap/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":276064331,"owners_count":25578999,"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":"2025-09-20T02:00:10.207Z","response_time":63,"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":["bioinformatics","genome-assembly","linkage","linkage-mapping","snakemake"],"created_at":"2024-12-08T22:17:39.664Z","updated_at":"2025-09-20T07:53:29.581Z","avatar_url":"https://github.com/pdimens.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"![logo](.misc/logo.png)\n\n_It's Lep-Map3 and Lep-Anchor, but with snakes 🐍🐍_\n\n[![alt text](https://img.shields.io/badge/docs-wiki-75ae6c?style=for-the-badge\u0026logo=Read%20The%20Docs)](https://github.com/pdimens/LepWrap/wiki) \n[![Cite](https://img.shields.io/badge/Cite-10.5281/zenodo.6055566-e1e1e1?style=for-the-badge)](https://doi.org/10.5281/zenodo.6055565) \n# LepWrap\n\nLepWrap is a reusable pipeline to use the linkage map software [Lep-Map3](https://sourceforge.net/projects/lep-map3/) and the genome assembly map-based anchoring and orienting software [Lep-Anchor](https://sourceforge.net/p/lep-anchor/wiki/Home/). Check out [the documentation/wiki](https://github.com/pdimens/LepWrap/wiki) for detailed installation, usage, and workflow information.\n\n### How to install\nYou will need a `conda` installation ([Anaconda](https://docs.anaconda.com/anaconda/install/) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html), I recommend Miniconda). Alternatively, you can download latest release or clone this repository locally (see wiki)\n\nCreate an environment called `lepwrap` and install `LepWrap` into it in a single command.\n```bash\nconda create -n lepwrap -c bioconda lepwrap\n```\nActivate the environment with `conda activate lepwrap`\n\nThis can also be done in an environment of your choosing\n```bash\nconda activate some_env\nconda install -c bioconda lepwrap\n```\n### How to run\nYou will need to modify `config.yml` to suit your needs, then you can simply run the pipeline with the wrapper:\n```bash\nLepWrap \u003cnumber_of_cores\u003e \u003cconfig.yml\u003e\n```\nwhere `\u003cnumber_of_cores\u003e` is an integer of the maximum number of cores/threads you want the pipeline to use and `\u003cconfig.yml\u003e` (optional!) is the name of the config file, if it's different than `config.yml`. If no config file is found in the directory, LepWrap will generate a default one for you to edit.\n\n**Examples**\n```bash\nLepWrap 15                    # assumes config.yml\nLepWrap 32 nojoinsingles.yml  # specific config file\n```\n### Something to keep in mind\nLepWrap does things a certain way, employing the most common/reasonable way of using Lep-Map3 (and LepAnchor, _more or less_). The current version is **a lot** more flexible that its predecessors, but might still lack something you need. Your study is unique, and I encourage you to clone/fork this repository and adapt LepWrap to it! All of the code in LepWrap is written in human-readable bash or aggressively annotated R, so give it a shot and adapt it to your workflow. PR's welcome!\n\n\n## Citation\nIf using LepWrap in a publication, cite **Pasi Rastas** for their work on Lep-Map3/Lep-Anchor and cite this repository using the Zenodo citation. You are also encouraged to cite LepWrap if you just use the edge-trimming part of it. If you like LepWrap, please Star the repository and/or give me (Pavel) a shout out on social media [mastodon](https://ecoevo.social/@pvdimens) [bluesky](https://bsky.app/profile/pvdimens.bsky.social)  =)\n\n\u003e Pavel V. Dimens. (2022). pdimens/LepWrap: link with zenodo (4.0). Zenodo. https://doi.org/10.5281/zenodo.6055565\n\n\u003e Pasi Rastas, Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data, Bioinformatics, Volume 33, Issue 23, 01 December 2017, Pages 3726–3732,https://doi.org/10.1093/bioinformatics/btx494\n\n\u003e Pasi Rastas, Lep-Anchor: automated construction of linkage map anchored haploid genomes, Bioinformatics, Volume 36, Issue 8, 15 April 2020, Pages 2359–2364, https://doi.org/10.1093/bioinformatics/btz978\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpdimens%2Flepwrap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpdimens%2Flepwrap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpdimens%2Flepwrap/lists"}