{"id":25282489,"url":"https://github.com/ngless-toolkit/ng-meta-profiler","last_synced_at":"2025-10-27T18:31:22.374Z","repository":{"id":137062012,"uuid":"133514900","full_name":"ngless-toolkit/ng-meta-profiler","owner":"ngless-toolkit","description":"Profiler for metagenomics based on NGLess","archived":false,"fork":false,"pushed_at":"2024-02-22T14:43:39.000Z","size":33,"stargazers_count":12,"open_issues_count":1,"forks_count":2,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-03-26T23:13:22.107Z","etag":null,"topics":["bioinformatics","metagenomics","microbiome","ngless"],"latest_commit_sha":null,"homepage":"https://ngless.embl.de","language":"Shell","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/ngless-toolkit.png","metadata":{"files":{"readme":"README.md","changelog":"ChangeLog","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.md","codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2018-05-15T12:46:00.000Z","updated_at":"2024-02-25T14:21:47.000Z","dependencies_parsed_at":"2023-03-21T11:03:53.555Z","dependency_job_id":null,"html_url":"https://github.com/ngless-toolkit/ng-meta-profiler","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ngless-toolkit%2Fng-meta-profiler","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ngless-toolkit%2Fng-meta-profiler/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ngless-toolkit%2Fng-meta-profiler/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ngless-toolkit%2Fng-meta-profiler/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ngless-toolkit","download_url":"https://codeload.github.com/ngless-toolkit/ng-meta-profiler/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":238536765,"owners_count":19488778,"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","metagenomics","microbiome","ngless"],"created_at":"2025-02-12T19:34:38.479Z","updated_at":"2025-10-27T18:31:22.089Z","avatar_url":"https://github.com/ngless-toolkit.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# NGLESS-PROFILER\n\n[https://ngless.embl.de](https://ngless.embl.de)\n\nThis is a collection of predefined [ngless](https://ngless.embl.de) pipelines\nfor processing shotgun metagenomes.\n\n1. `human-gut.ngl` for human gut samples\n\n2. `marine.ngl` for marine samples\n\n3. `mouse-gut.ngl` for mouse gut samples\n\n4. `dog-gut.ngl` for dog gut samples\n\n5. `pig-gut.ngl` for pig gut samples\n\nThese are predefined, but users are encouraged to adapt them to their specific\nneeds.\n\n## Citation\n\nIf you are using NG-meta-profiler (or any NGLess-based pipeline), please cite:\n\n\u003e _NG-meta-profiler: fast processing of metagenomes using NGLess, a\n\u003e domain-specific language_ by Luis Pedro Coelho, Renato Alves, Paulo Monteiro,\n\u003e Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork, Microbiome (2019)\n\u003e [https://doi.org/10.1186/s40168-019-0684-8](https://doi.org/10.1186/s40168-019-0684-8)\n\n\n## INSTALL\n\nYou need to\n\n1. install [ngless](https://github.com/ngless-toolkit/ngless). The recommended\n   way is through bioconda:\n\n    conda install -c bioconda ngless\n\nAlternatively, see the [ngless documentation on how to install\nit](https://ngless.embl.de/install.html).\n\n2. copy the profiling scripts to next to where your data lives\n\n\n## USAGE\n\nTo use the profiler, select the appropriate script (e.g., `human-gut.ngl` for\nhuman gut samples), put all the FastQ files from the same sample in the same\ndirectory (`INPUT-DIRECTORY`) with the extension `.fq.gz` or `fastq.gz` and\nrun:\n\n    ngless human-gut.ngl INPUT-DIRECTORY OUTPUT-DIRECTORY\n\nYou can use all the [ngless command line\noptions](https://ngless.embl.de/command-line-options.html) to set options. For\nexample, to use 8 cores, use:\n\n    ngless --threads=8 human-gut.ngl INPUT-DIRECTORY OUTPUT-DIRECTORY\n\nIf you want very verbose output:\n\n    ngless --threads=8 --trace human-gut.ngl INPUT-DIRECTORY OUTPUT-DIRECTORY\n\n### USAGE WITH DOCKER\n\nWe now also provide docker containers containing all required databases on\n[docker hub](https://cloud.docker.com/u/nglesstoolkit/).\n\nThese images can be used directly or through the convenience script\n[ng-meta-profiler.sh](https://github.com/ngless-toolkit/ng-meta-profiler/blob/master/ng-meta-profiler.sh).\nTo use `ng-meta-profiler.sh` simply download the script, decide which profiler\nto use (`human-gut:1.0.0` in the example) and run:\n\n    ng-meta-profiler.sh human-gut:1.0.0 INPUT-DIRECTORY OUTPUT-DIRECTORY\n\nwhich will download and analyse the specified data with the `human-gut:1.0.0` profiler.\n\n`INPUT` and `OUTPUT` should be absolute paths and `INPUT` should be a directory\ncontaining a metagenome as a set of files named according to the [MOCAT\nformat](https://ngless.embl.de/stdlib.html#mocat-module).\n\n## RESOURCE REQUIREMENTS\n\n| Profiler | Memory | Disk space |\n|----------|--------|------------|\n| Human    |  14.7G |       18G  |\n| Mouse    |   5.1G |      6.3G  |\n| Dog      |   4.5G |      3.5G  |\n| Pig      |  10.1G |       17G  |\n\nNote too that _the first time_ you run a particular profiler, NGLess will\ndownload and index the respective databases. This is likely to take several\nhours (and this process does not benefit from using multiple threads). This is\nonly necessary once. Afterwards, the index will be reused (this is what is\nresponsible for disk space usage in the table above).\n\n## GETTING HELP\n\n- [NGLess webpage](https://ngless.embl.de) includes a section on [ngless-profiler]()\n- For questions, you can use the [ngless mailing\n  list](https://groups.google.com/forum/#!forum/ngless).\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fngless-toolkit%2Fng-meta-profiler","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fngless-toolkit%2Fng-meta-profiler","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fngless-toolkit%2Fng-meta-profiler/lists"}