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16smart

16s rRNA Sequencing Meta-analysis Reproducibility Tool (using mothur).

https://github.com/achillesrasquinha/16smart

Science Score: 26.0%

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    Low similarity (15.3%) to scientific vocabulary

Keywords

16s-rrna bioinformatics meta-analysis mothur python reproducible-research sequencing
Last synced: 6 months ago · JSON representation

Repository

16s rRNA Sequencing Meta-analysis Reproducibility Tool (using mothur).

Basic Info
  • Host: GitHub
  • Owner: achillesrasquinha
  • License: mit
  • Language: Python
  • Default Branch: develop
  • Homepage:
  • Size: 2.77 MB
Statistics
  • Stars: 7
  • Watchers: 2
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Topics
16s-rrna bioinformatics meta-analysis mothur python reproducible-research sequencing
Created over 4 years ago · Last pushed about 3 years ago
Metadata Files
Readme License Citation Authors

README.md

16SMaRT

16s rRNA Sequencing Meta-analysis Reconstruction Tool.

**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. 16SMaRT is written in Python using [boilpy's](https://github.com/achillesrasquinha/boilpy) data-pipeline boilerplate. 16SMaRT 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).

Table of Contents

Features

Quick Start

Using Docker

First, install docker onto your system (can be followed via docker's documentation).

Then, you can run simply run 16SMaRT by the following command:

docker run \ --rm -it \ -v "<HOST_MACHINE_PATH_DATA>:/data" \ -v "<HOST_MACHINE_PATH_CONFIG>:/root/.config/s3mart \ -v "<HOST_MACHINE_PATH_WORKSPACE>:/work \ ghcr.io/achillesrasquinha/s3mart \ bpyutils --run-ml s3mart -p "data_dir=/data" --verbose

where <HOST_MACHINE_PATH_DATA> is the path to your host machine to store pipeline data and <HOST_MACHINE_PATH_CONFIG> is the path to store 16SMaRT configuration and intermediate data. <HOST_MACHINE_PATH_WORKSPACE> is a workspace directory for you to store your files that can be used by 16SMaRT (e.g. input files).

Running on HPC systems using Singularity

Singularity 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.

singularity run \ --home $HOME \ --cleanenv \ -B <HOST_MACHINE_PATH_DATA>:/data \ -B <HOST_MACHINE_PATH_CONFIG>:/root/.config/s3mart \ -B <HOST_MACHINE_PATH_WORKSPACE>:/work \ oras://ghcr.io/achillesrasquinha/s3mart:singularity \ bpyutils --run-ml s3mart -p "data_dir=/data" --verbose

Usage

Basic Usage

  • input

    Path to input CSV file, data directory of FASTQ files, URL to CSV file.

  • fastqc

    Run FASTQC after downloading SRAs. (boolean, default - True)

  • multiqc

    Run MultiQC after performing FASTQC. (boolean, default - True)

Check out the docs page to understand how to use this pipeline.

Support

Have any queries? Post an issue on the GitHub Issue Tracker.

Citation

If you use this software in your work, please cite it using the following:

Furbeck, R., & Rasquinha, A. (2021). 16SMaRT - 16s rRNA Sequencing Meta-analysis Reconstruction Tool. (Version 0.1.0) [Computer software]. https://github.com/achillesrasquinha/16SMaRT

A comprehensive list of references for the tools used is listed here.

License

This repository has been released under the MIT License.

Made with ❤️ using boilpy.

Owner

  • Name: Achilles Rasquinha
  • Login: achillesrasquinha
  • Kind: user
  • Location: Madison, Wisconsin
  • Company: @aws

I write code that automates my job.

GitHub Events

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  • Total issues: 3
  • Total pull requests: 0
  • Average time to close issues: 4 days
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  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
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  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • achillesrasquinha (2)
  • furbeck (1)
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Issue Labels
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Pull Request Labels

Dependencies

requirements/development.txt pypi
  • Flask * development
  • bumpversion * development
  • ipython * development
  • jedi <0.18 development
  • jupyter * development
  • pipenv * development
  • pre-commit * development
  • safety * development
  • twine * development
  • vulture * development
requirements/documentation.txt pypi
  • ipykernel *
  • nbsphinx *
  • recommonmark *
  • sphinx *
  • sphinx-autobuild *
requirements/lint.txt pypi
  • autopep8 *
  • pylint *
requirements/production.txt pypi
  • BioPython *
  • bpyutils *
  • cutadapt *
  • jinja2 *
  • multiqc *
  • parallel-fastq-dump *
  • requests *
  • rpy2 *
  • tqdm *
requirements/test.txt pypi
  • coveralls * test
  • docstr-coverage * test
  • pluggy <1,>=0.12.0 test
  • pytest * test
  • pytest-clarity * test
  • pytest-cov * test
  • pytest-sugar * test
  • pytest-xdist * test
  • tox * test
requirements-dev.txt pypi
  • BioPython * development
  • Flask * development
  • autopep8 * development
  • bpyutils * development
  • bumpversion * development
  • coveralls * development
  • cutadapt * development
  • docstr-coverage * development
  • ipykernel * development
  • ipython * development
  • jedi <0.18 development
  • jinja2 * development
  • jupyter * development
  • multiqc * development
  • nbsphinx * development
  • parallel-fastq-dump * development
  • pipenv * development
  • pluggy <1,>=0.12.0 development
  • pre-commit * development
  • pylint * development
  • pytest * development
  • pytest-clarity * development
  • pytest-cov * development
  • pytest-sugar * development
  • pytest-xdist * development
  • recommonmark * development
  • requests * development
  • rpy2 * development
  • safety * development
  • sphinx * development
  • sphinx-autobuild * development
  • tox * development
  • tqdm * development
  • twine * development
  • vulture * development
requirements-jobs.txt pypi
  • BioPython *
  • Flask *
  • autopep8 *
  • bpyutils *
  • bumpversion *
  • coveralls *
  • cutadapt *
  • docstr-coverage *
  • ipykernel *
  • ipython *
  • jedi <0.18
  • jinja2 *
  • jupyter *
  • multiqc *
  • nbsphinx *
  • parallel-fastq-dump *
  • pipenv *
  • pluggy <1,>=0.12.0
  • pre-commit *
  • pylint *
  • pytest *
  • pytest-clarity *
  • pytest-cov *
  • pytest-sugar *
  • pytest-xdist *
  • recommonmark *
  • requests *
  • rpy2 *
  • safety *
  • sphinx *
  • sphinx-autobuild *
  • tox *
  • tqdm *
  • twine *
  • vulture *
requirements.txt pypi
  • BioPython *
  • bpyutils *
  • cutadapt *
  • jinja2 *
  • multiqc *
  • parallel-fastq-dump *
  • requests *
  • rpy2 *
  • tqdm *
.github/workflows/boilpy.yml actions
  • achillesrasquinha/boilpy-action develop composite
.github/workflows/ci.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/docker.yml actions
  • actions/checkout v2 composite
.github/workflows/jobs.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/model-ci.yml actions
  • actions/checkout v2 composite
  • actions/upload-artifact v2 composite
Dockerfile docker
  • ghcr.io/achillesrasquinha/s3mart base build
docker/files/base/Dockerfile docker
  • python 3.9 build