This Snakemake pipeline dedicated to Metagenomic data analysis consists out of several modules that cover a) read-based b) contig-based and c) MAG-based analyses as well as quantification, quality checks and a reporting module (which is currently under development). Naturally, it runs seamlessly on HPC systems and all required software tools are bundled in docker container and/or conda environments. Further, all required databases are pre-configured and ready to be downloaded from a central place.
This makes it straight forward and as user-friendly as it can get.
The pipeline is organised in modules, which can run one-by-one. Further, the user can also choose to run individual tools, giving full flexibility on how to use and run the pipeline.
For a step-by-step tutorial on how to install the pipeline and all pre-compiled databases, please see
Guide to install the pipeline: Installation
Guide to prepare the configuration files: Setup
Guide for running the pipeline: Usage
For troubleshooting, please visit the collection of most common errors: Troubleshooting
List of contributing authors: ...
Please use the issue tracker from the GitHub or contact one of the contributors, if you'd prefer personal contact.
fastpkraken2SingleMNonpareilbowtie2samtoolsMEGAHITCONCOCTMaxBin2MetaBat2MAGScoTdRepQUASTGTDB-TKDRAMCoverMFastQCmultiqc
This pipeline is a fork from the Snakemake workflow
https://github.com/3d-omics/mg_assembly/
and tailored and extended to the needs of the Holoruminant project.