niekwit/damid-seq

Snakemake workflow for DamID-Seq analysis

Snakemake workflow: damid-seq

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).

Aim

damid-seq is a containerized Snakemake pipeline for reproducible and scalable analysis of single/paired-end DamID-seq short read Illumina data.

Documentation

Documentation of how to use damid-seq can be found at https://damid-seq.readthedocs.io/en/latest/.

Overview of documentation

• 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
  • Archive of the analysis
• Output files
  • Quality control
  • Visualization of damid-seq data
  • Peak-related plots
• Citation
  • Workflow
  • Software used in workflow
• literature
  • DamID
• Source code
  • Reporting issues