If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (see above).
damid-seq is a containerized Snakemake pipeline for reproducible analysis of single/paired-end DamID-seq short read Illumina data.
The core of the pipeline is the Perl script damidseq_pipeline, which is a great tool for the first steps of analysing DamID-seq data. However, it does not process biological replicate data, and is not written with deployment to server, cluster, grid and cloud environments in mind.
damid-seq implements the Snakemake workflow management system, which overcomes the above issues. In addition, we have added many features to the DamID-seq analysis workflow.
Documentation of how to use damid-seq can be found at https://damid-seq.readthedocs.io/en/latest/.
- DamID
- DamID principle
- Experimental considerations
- Software requirements
- Conda/Mamba
- Snakemake
- Apptainer
- Snakefetch
- Usage
- Preparing raw sequencing data
- Sample meta data and analysis settings
- Configuration of Snakemake
- Dry-run of the analysis
- Visualization of the workflow
- Running the analysis
- Report of the results
- Output
- Quality control
- Visualization of damid-seq data
- Peaks
- Citation
- Workflow
- Software used in workflow