{"id":22367964,"url":"https://github.com/dridk/mucobiome","last_synced_at":"2026-02-26T08:33:01.606Z","repository":{"id":74195584,"uuid":"52479577","full_name":"dridk/mucobiome","owner":"dridk","description":"A simple 16S  RNA pipeline ","archived":false,"fork":false,"pushed_at":"2019-01-13T20:05:45.000Z","size":1245,"stargazers_count":3,"open_issues_count":1,"forks_count":0,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-01-31T17:52:33.637Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"HTML","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/dridk.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":"2016-02-24T22:38:16.000Z","updated_at":"2019-01-13T20:05:47.000Z","dependencies_parsed_at":"2023-05-27T17:00:15.071Z","dependency_job_id":null,"html_url":"https://github.com/dridk/mucobiome","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dridk%2Fmucobiome","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dridk%2Fmucobiome/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dridk%2Fmucobiome/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dridk%2Fmucobiome/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dridk","download_url":"https://codeload.github.com/dridk/mucobiome/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245689509,"owners_count":20656417,"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":[],"created_at":"2024-12-04T18:25:26.398Z","updated_at":"2026-02-26T08:32:56.584Z","avatar_url":"https://github.com/dridk.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Mucobiome ![GitHub Logo](https://img.shields.io/badge/snakemake-≥3.5.2-brightgreen.svg?style=flat-square)\n\nMucobiome is a simple pipeline which aims to analyse 16S RNA genomics data from high throughput sequencer.\nNeither QIIME nor MOTHUR are required. Few dependency like vsearch are necessary and are listed bellow.\nMucobiome use [snakemake](https://bitbucket.org/johanneskoester/snakemake/wiki/Home) as the backbone. This tools make it possible to run\nthe pipeline optimally using multithreading. \n\n## How it works ? **Fastq paired files** -\u003e **biom**   \n  \nthe pipeline takes several pair-end fastq as input ( one per sample) and generate one biom file which contains OTU table with taxonomy and sample \nmeta data. \n - For each reads pairs :\n  - Merge fastq file using vsearch or flash \n  - Clean fastq file using sickle \n  - Reverse reads with seqtk  \n  - Trim adaptators from reads using cutadapts \n  - Dereplicate reads with vsearch \n  - merge all reads pairs into one fasta file \n - With Greengene database \n  - Extract interesting region from greengene 16S database using cutadapts and user's adaptator \n - Make a taxonomy assignement using vsearch --usearch_global\n  - Compare sequence from the merged file and greengene database\n  - Create a Biom file\n  - Add taxonomy and sample metadata into the biom file\n\n\n## Installation \n### Python depedencies \nMucobiome has been written with Python 3.4. \n\n    pip install -r requirements.txt \n\n### Install vsearch\n```\nwget https://github.com/torognes/vsearch/archive/v2.3.4.tar.gz\ntar xzf v2.3.4.tar.gz\ncd vsearch-2.3.4\n./autogen.sh\n./configure\nmake\nmake install  # as root or sudo make install\n```\n\n### Install seqtk\n```\ngit clone https://github.com/lh3/seqtk.git;\ncd seqtk;\nmake\nsudo make install\n```\n\n### Install sickle \n```\nhttps://github.com/najoshi/sickle.git\ncd sickle\nmake\nsudo make install\n```\n\n## Download Database \nMucobiome works with greengene. But you can use another database if you respect the same format. \nRun download_greengene.sh from the database folder to download greengene data. \n\n     cd database; sh download_greengene.sh \n     \n## usage \n### Test your installation \nThe actual repositories contains a simple dataset. Try the following commands which do nothing but display all pipeline command.\n\n```\n# you are in the main directory \nsnakemake -d working_directory -np --configfile config.yaml\n```\n\u003ctable\u003e\n\u003ctr\u003e\u003cth\u003eOptions\u003c/th\u003e\u003cth\u003eDescription\u003c/th\u003e\u003c/tr\u003e\n\u003ctr\u003e\u003cth\u003e-d\u003c/th\u003e\u003ctd\u003eThe working directory. All generated files will be drop here\u003c/td\u003e\u003c/tr\u003e\n\u003ctr\u003e\u003cth\u003e-n\u003c/th\u003e\u003ctd\u003eDon't execute any commands.\u003c/td\u003e\u003c/tr\u003e\n\u003ctr\u003e\u003cth\u003e-p\u003c/th\u003e\u003ctd\u003ePrint commands\u003c/td\u003e\u003c/tr\u003e\n\u003ctr\u003e\u003cth\u003e--configfile\u003c/th\u003e\u003ctd\u003eTell which config file to use\u003c/td\u003e\u003c/tr\u003e\n\u003c/table\u003e\n\n### Input file \ninput data are paired fastq.gz files. You must put all your datas into the data/raw folder. Both paired files must respect the following syntax.\n*{Sample}* is your samplename. Do not use \".\" character in sample name. use alpha numeric only .\n\n     {SAMPLE}_1.fastq.gz \n     {SAMPLE}_2.fastq.gz\n\n### config.yaml \nThis file contains all parameters required to perform an analysis. \n\n\u003ctable\u003e\n\u003ctr\u003e\u003cth\u003eOptions\u003c/th\u003e\u003cth\u003eDescription\u003c/th\u003e\u003c/tr\u003e\n\u003ctr\u003e\u003cth\u003eraw_folder\u003c/th\u003e\u003ctd\u003ethe directory which contains fastq input files\u003c/td\u003e\u003c/tr\u003e\n\u003ctr\u003e\u003cth\u003eprimer_forward\u003c/th\u003e\u003ctd\u003eThe forward primer. By defaut primers select the V3-V5 region\u003c/td\u003e\u003c/tr\u003e\n\u003ctr\u003e\u003cth\u003ereverse_primer\u003c/th\u003e\u003ctd\u003eThe reverse primer. By defaut primers select the V3-V5 region\u003c/td\u003e\u003c/tr\u003e\n\u003ctr\u003e\u003cth\u003edatabase_fasta\u003c/th\u003e\u003ctd\u003eThis is a fasta file which contains complete 16S sequence. By default it use greengene\u003c/td\u003e\u003c/tr\u003e\n\u003ctr\u003e\u003cth\u003edatabase_taxonomy\u003c/th\u003e\u003ctd\u003eThis is a two columns file. Fasta header ID from database_fasta and the taxonomy\u003c/td\u003e\u003c/tr\u003e\n\u003ctr\u003e\u003cth\u003esample_data\u003c/th\u003e\u003ctd\u003eSample meta data\u003c/td\u003e\u003c/tr\u003e\n\u003ctr\u003e\u003cth\u003ethreshold\u003c/th\u003e\u003ctd\u003eTaxonomy assignement threshold. By default 97%\u003c/td\u003e\u003c/tr\u003e\n\u003ctr\u003e\u003cth\u003equality\u003c/th\u003e\u003ctd\u003eRemove all reads bellow this threshold. You should set this value to 20\u003c/td\u003e\u003c/tr\u003e\n\u003ctr\u003e\u003cth\u003emin_len\u003c/th\u003e\u003ctd\u003eMinimum reads length accepted\u003c/td\u003e\u003c/tr\u003e\n\u003ctr\u003e\u003cth\u003emax_len\u003c/th\u003e\u003ctd\u003eMaximum reads length accepted\u003c/td\u003e\u003c/tr\u003e\n\u003ctr\u003e\u003cth\u003emerge_tool\u003c/th\u003e\u003ctd\u003eUse Flash or vsearch to perform merging. By default it use vsearch\u003c/td\u003e\u003c/tr\u003e\n\u003c/table\u003e\n\n### sample_data.tsv\nThis files contains metadata for each sample. Fill it with your own data. \n\n\n### Run your experiment \nWhen all requirements are done, you can run one of the following commands\n\n       # Run your pipeline using 60 threads\n       snakemake -d working_directory -p --configfile config.yaml --cores 60\n       \n       # Force the pipeline to rebuild the last step\n       snakemake -d working_directory -fp --configfile config.yaml --cores 60\n       \n       # Force the pipeline to rebuild everything\n       snakemake -d working_directory -Fp --configfile config.yaml --cores 60\n\n\n     \n\n\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdridk%2Fmucobiome","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdridk%2Fmucobiome","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdridk%2Fmucobiome/lists"}