https://github.com/fischuu/snakebite-holoruminant-metag
Easy to use Snakemake metagenomic pipeline that covers a) read-based analysis b) contig based analysis and c) MAG assembly and annotation using a broad set of ready to use and included public databases and annotators
https://github.com/fischuu/snakebite-holoruminant-metag
dna metagenome-assembled-genomes metagenomics snakemake snakemake-workflow
Last synced: 4 months ago
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Easy to use Snakemake metagenomic pipeline that covers a) read-based analysis b) contig based analysis and c) MAG assembly and annotation using a broad set of ready to use and included public databases and annotators
- Host: GitHub
- URL: https://github.com/fischuu/snakebite-holoruminant-metag
- Owner: fischuu
- Created: 2024-05-15T12:06:30.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2026-01-31T06:15:49.000Z (4 months ago)
- Last Synced: 2026-01-31T20:17:52.968Z (4 months ago)
- Topics: dna, metagenome-assembled-genomes, metagenomics, snakemake, snakemake-workflow
- Language: HTML
- Homepage:
- Size: 26.5 MB
- Stars: 9
- Watchers: 3
- Forks: 1
- Open Issues: 20
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG
- Citation: citations.tct
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README
# Overview
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.
# Installation, Setup and running 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](https://github.com/fischuu/Pipeline-Holoruminant-Meta/blob/main/docs/02-Installation.md)
Guide to prepare the configuration files: [Setup](https://github.com/fischuu/Pipeline-Holoruminant-Meta/blob/main/docs/03-Setup.md)
Guide for running the pipeline: [Usage](https://github.com/fischuu/Pipeline-Holoruminant-Meta/blob/main/docs/04-Usage.md)
Information for additional tools: [Extra](https://github.com/fischuu/Pipeline-Holoruminant-Meta/blob/main/docs/05-Extra.md)
For troubleshooting, please visit the collection of most common errors: [Troubleshooting](https://github.com/fischuu/Pipeline-Holoruminant-Meta/blob/main/docs/10-Troubleshooting.md)
# Contributions
List of contributing authors:
...
# Contact
Please use the issue tracker from the GitHub or contact one of the contributors, if you'd prefer personal contact.
## References
- [`fastp`](https://github.com/OpenGene/fastp)
- [`kraken2`](https://github.com/DerrickWood/kraken2)
- [`SingleM`](https://github.com/wwood/singlem)
- [`Nonpareil`](https://github.com/lmrodriguezr/nonpareil)
- [`bowtie2`](https://github.com/BenLangmead/bowtie2)
- [`samtools`](https://github.com/samtools/samtools)
- [`MEGAHIT`](https://github.com/voutcn/megahit)
- [`CONCOCT`](https://github.com/BinPro/CONCOCT)
- [`MaxBin2`](http://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html)
- [`MetaBat2`](https://bitbucket.org/berkeleylab/metabat)
- [`MAGScoT`](https://github.com/ikmb/MAGScoT)
- [`dRep`](https://github.com/MrOlm/drep)
- [`QUAST`](https://github.com/ablab/quast)
- [`GTDB-TK`](https://github.com/Ecogenomics/GTDBTk)
- [`DRAM`](https://github.com/WrightonLabCSU/DRAM)
- [`CoverM`](https://github.com/wwood/CoverM)
- [`FastQC`](https://github.com/s-andrews/FastQC)
- [`multiqc`](https://github.com/ewels/MultiQC)
- [`NCyc`](https://github.com/qichao1984/NCyc)
# Acknowledgements
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.