{"id":20109748,"url":"https://github.com/achillesrasquinha/16smart","last_synced_at":"2025-05-06T10:31:37.451Z","repository":{"id":58186682,"uuid":"415375504","full_name":"achillesrasquinha/16SMaRT","owner":"achillesrasquinha","description":"16s rRNA Sequencing Meta-analysis Reproducibility Tool (using mothur).","archived":false,"fork":false,"pushed_at":"2022-11-26T22:05:52.000Z","size":2909,"stargazers_count":7,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"develop","last_synced_at":"2025-04-13T02:42:56.498Z","etag":null,"topics":["16s-rrna","bioinformatics","meta-analysis","mothur","python","reproducible-research","sequencing"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/achillesrasquinha.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS.md","dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2021-10-09T17:22:20.000Z","updated_at":"2024-07-28T03:20:19.000Z","dependencies_parsed_at":"2023-01-23T16:01:12.244Z","dependency_job_id":null,"html_url":"https://github.com/achillesrasquinha/16SMaRT","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/achillesrasquinha%2F16SMaRT","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/achillesrasquinha%2F16SMaRT/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/achillesrasquinha%2F16SMaRT/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/achillesrasquinha%2F16SMaRT/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/achillesrasquinha","download_url":"https://codeload.github.com/achillesrasquinha/16SMaRT/tar.gz/refs/heads/develop","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252665995,"owners_count":21785182,"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":["16s-rrna","bioinformatics","meta-analysis","mothur","python","reproducible-research","sequencing"],"created_at":"2024-11-13T18:09:21.039Z","updated_at":"2025-05-06T10:31:35.915Z","avatar_url":"https://github.com/achillesrasquinha.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cdiv align=\"center\"\u003e\n  \u003cimg src=\".github/assets/logo.png\" height=\"200\"\u003e\n  \u003ch1\u003e\n      16SMaRT\n  \u003c/h1\u003e\n  \u003ch4\u003e16s rRNA Sequencing Meta-analysis Reconstruction Tool.\u003c/h4\u003e\n\u003c/div\u003e\n\n\u003cp align=\"center\"\u003e\n    \u003ca href='https://github.com/achillesrasquinha/16SMaRT/actions?query=workflow:\"Model CI\"'\u003e\n      \u003cimg src=\"https://img.shields.io/github/workflow/status/achillesrasquinha/16SMaRT/Model CI?style=flat-square\"\u003e\n    \u003c/a\u003e\n    \u003ca href='https://github.com/achillesrasquinha/16SMaRT/actions?query=workflow:\"Docker\"'\u003e\n      \u003cimg src=\"https://img.shields.io/github/workflow/status/achillesrasquinha/16SMaRT/Docker?style=flat-square\u0026label=docker\"\u003e\n    \u003c/a\u003e\n    \u003ca href=\"https://git.io/boilpy\"\u003e\n      \u003cimg src=\"https://img.shields.io/badge/made%20with-boilpy-red.svg?style=flat-square\"\u003e\n    \u003c/a\u003e\n\u003c/p\u003e\n\n\u003cdiv align=\"justify\"\u003e\n\n**16SMaRT** is a bioinformatics analysis pipeline for 16s rRNA gene sequencing data. 16SMaRT is a \"one-click\" solution towards performing microbial community analysis of amplicon sequencing data. 16SMaRT aims to be your go-to solution for your next microbiome/metagenomics project. The primary objective of 16SMaRT analysis is to determine what genes are present and in what proportions in comparison across a range of samples. It currently supports single-end or paired-end [Illumina](https://www.illumina.com/) MiSeq data.\n\n16SMaRT is written in Python using [boilpy's](https://github.com/achillesrasquinha/boilpy) data-pipeline boilerplate. \n16SMaRT is built on top of a considerable amount of dependencies and hence, the recommended way to install it is by using [docker](#using-docker) thus making installation in \"one-click\" and perfectly reproducible results. 16SMaRT is built with considering maximizing computation resources in mind thereby making it blazingly fast even on a local machine for a decent amount of samples. For a large number of studies, it is recommended to run 16SMaRT on a High-Performance Computing system using [singularity](#running-on-hpc-systems-using-singularity).\n\n\u003c/div\u003e\n\n## Table of Contents\n\n* [Features](#features)\n* [Quick Start](#quick-start)\n* [Usage](#usage)\n* [Support](#support)\n* [Citation](#citation)\n* [License](#license)\n\n## Features\n\n* Supports single-end and paired-end [Illumina](https://www.illumina.com/) data.\n* Quality Control using [FASTQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and [MultiQC](https://multiqc.info/).\n* Trimming using [mothur](https://mothur.org).\n* Analysis using [phyloseq](https://joey711.github.io/phyloseq/).\n* Multi-Processing.\n* [Docker](https://www.docker.com/) + [Singularity](https://singularity.hpcng.org/) support.\n\n## Quick Start\n\n### Using [Docker](https://www.docker.com/)\n\nFirst, install docker onto your system (can be followed via [docker's documentation](https://docs.docker.com/engine/install)).\n\nThen, you can run simply run 16SMaRT by the following command:\n\n```\ndocker run \\\n    --rm -it \\\n    -v \"\u003cHOST_MACHINE_PATH_DATA\u003e:/data\" \\\n    -v \"\u003cHOST_MACHINE_PATH_CONFIG\u003e:/root/.config/s3mart \\\n    -v \"\u003cHOST_MACHINE_PATH_WORKSPACE\u003e:/work \\\n    ghcr.io/achillesrasquinha/s3mart \\\n    bpyutils --run-ml s3mart -p \"data_dir=/data\" --verbose\n```\n\nwhere `\u003cHOST_MACHINE_PATH_DATA\u003e` is the path to your host machine to store pipeline data and `\u003cHOST_MACHINE_PATH_CONFIG\u003e` is the path to store 16SMaRT configuration and intermediate data. `\u003cHOST_MACHINE_PATH_WORKSPACE\u003e` is a workspace directory for you to store your files that can be used by 16SMaRT (e.g. input files).\n\n### Running on HPC systems using [Singularity](https://singularity.hpcng.org/)\n\nSingularity is the most widely used container system for HPC (High-Performance Computing) systems. In order to run your analysis on an HPC system, simply run the following command.\n\n```\nsingularity run \\\n    --home $HOME \\\n    --cleanenv \\\n    -B \u003cHOST_MACHINE_PATH_DATA\u003e:/data \\\n    -B \u003cHOST_MACHINE_PATH_CONFIG\u003e:/root/.config/s3mart \\\n    -B \u003cHOST_MACHINE_PATH_WORKSPACE\u003e:/work \\\n    oras://ghcr.io/achillesrasquinha/s3mart:singularity \\\n    bpyutils --run-ml s3mart -p \"data_dir=/data\" --verbose\n```\n\n## Usage\n\n### Basic Usage\n\n* [**`input`**]()\n\n    *Path to input CSV file, data directory of FASTQ files, URL to CSV file.*\n\n* [**`fastqc`**]()\n\n    *Run FASTQC after downloading SRAs.* (boolean, default - `True`)\n\n* [**`multiqc`**]()\n\n    *Run MultiQC after performing FASTQC.* (boolean, default - `True`)\n\n\nCheck out the [docs](docs/source) page to understand how to use this pipeline.\n\n## Support\n\nHave any queries? Post an issue on the [GitHub Issue Tracker](https://github.com/achillesrasquinha/16SMaRT/issues).\n\n## Citation\n\nIf you use this software in your work, please cite it using the following:\n\n\u003e Furbeck, R., \u0026 Rasquinha, A. (2021). 16SMaRT - 16s rRNA Sequencing Meta-analysis Reconstruction Tool. (Version 0.1.0) [Computer software]. [https://github.com/achillesrasquinha/16SMaRT](https://github.com/achillesrasquinha/16SMaRT)\n\nA comprehensive list of references for the tools used is listed [here](REFERENCES.md).\n\n## License\n\nThis repository has been released under the [MIT License](LICENSE).\n\n---\n\n\u003cdiv align=\"center\"\u003e\n  Made with ❤️ using \u003ca href=\"https://git.io/boilpy\"\u003eboilpy\u003c/a\u003e.\n\u003c/div\u003e","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fachillesrasquinha%2F16smart","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fachillesrasquinha%2F16smart","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fachillesrasquinha%2F16smart/lists"}