Research Object Crate for SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes
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All you have to do now is to indicate the path to the database folder (in our example, the folder is called release207_v2) in the config file, Classification section.
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All you have to do now is to indicate the path to the GUNC database file in the config file, Bins quality section.
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Research Object Crate for SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes
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date created: 2023-09-08 12:14:52.655671+00:00
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description: [![Snakemake](https://img.shields.io/badge/snakemake-≥7.0.0-brightgreen.svg?style=flat)](https://snakemake.readthedocs.io) # About SnakeMAGs SnakeMAGs is a workflow to reconstruct prokaryotic genomes from metagenomes. The main purpose of SnakeMAGs is to process Illumina data from raw reads to metagenome-assembled genomes (MAGs). SnakeMAGs is efficient, easy to handle and flexible to different projects. The workflow is CeCILL licensed, implemented in Snakemake (run on multiple cores) and available for Linux. SnakeMAGs performed eight main steps: - Quality filtering of the reads - Adapter trimming - Filtering of the host sequences (optional) - Assembly - Binning - Evaluation of the quality of the bins - Classification of the MAGs - Estimation of the relative abundance of the MAGs ![scheme of workflow](SnakeMAGs_schema.jpg?raw=true) # How to use SnakeMAGs ## Install conda The easiest way to install and run SnakeMAGs is to use [conda](https://www.anaconda.com/products/distribution). These package managers will help you to easily install [Snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html). ## Install and activate Snakemake environment Note: The workflow was developed with Snakemake 7.0.0 ``` conda activate # First, set up your channel priorities conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge # Then, create a new environment for the Snakemake version you require conda create -n snakemake_7.0.0 snakemake=7.0.0 # And activate it conda activate snakemake_7.0.0 ``` Alternatively, you can also install Snakemake via mamba: ``` # If you do not have mamba yet on your machine, you can install it with: conda install -n base -c conda-forge mamba # Then you can install Snakemake conda activate base mamba create -c conda-forge -c bioconda -n snakemake snakemake # And activate it conda activate snakemake ``` ## SnakeMAGs executable The easiest way to procure SnakeMAGs and its relate…
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SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes
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description: [![Snakemake](https://img.shields.io/badge/snakemake-≥7.0.0-brightgreen.svg?style=flat)](https://snakemake.readthedocs.io) # About SnakeMAGs SnakeMAGs is a workflow to reconstruct prokaryotic genomes from metagenomes. The main purpose of SnakeMAGs is to process Illumina data from raw reads to metagenome-assembled genomes (MAGs). SnakeMAGs is efficient, easy to handle and flexible to different projects. The workflow is CeCILL licensed, implemented in Snakemake (run on multiple cores) and available for Linux. SnakeMAGs performed eight main steps: - Quality filtering of the reads - Adapter trimming - Filtering of the host sequences (optional) - Assembly - Binning - Evaluation of the quality of the bins - Classification of the MAGs - Estimation of the relative abundance of the MAGs ![scheme of workflow](SnakeMAGs_schema.jpg?raw=true) # How to use SnakeMAGs ## Install conda The easiest way to install and run SnakeMAGs is to use [conda](https://www.anaconda.com/products/distribution). These package managers will help you to easily install [Snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html). ## Install and activate Snakemake environment Note: The workflow was developed with Snakemake 7.0.0 ``` conda activate # First, set up your channel priorities conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge # Then, create a new environment for the Snakemake version you require conda create -n snakemake_7.0.0 snakemake=7.0.0 # And activate it conda activate snakemake_7.0.0 ``` Alternatively, you can also install Snakemake via mamba: ``` # If you do not have mamba yet on your machine, you can install it with: conda install -n base -c conda-forge mamba # Then you can install Snakemake conda activate base mamba create -c conda-forge -c bioconda -n snakemake snakemake # And activate it conda activate snakemake ``` ## SnakeMAGs executable The easiest way to procure SnakeMAGs and its relate…
keywords: Bioinformatics, Metagenomics, binning, MAG
license: no-permission
producer: Metagenomic tools
programming language: #snakemake
sd date published: 2023-08-02 11:41:06+00:00
sd publisher: https://about.workflowhub.eu/
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