SnakeChunks¶
This git repository holds shared code for the analysis of Next Generation Sequencing data related to gene regulation: ChIP-seq, RNA-seq, and related technologies.
It was developed as part of the France Genomique Workpackage 2.6: Gene expression regulation.
One of the key goals is to ensure portability and re-usability of the code.
We have chosen to use the Snakemake workflow management system[1] in order to build reproducible and flexible NGS analysis pipelines.
Contact¶
- Claire Rioualen claire.rioualen@inserm.fr
- Jacques van Helden Jacques.van-helden@univ-amu.fr
References¶
- Köster, Johannes and Rahmann, Sven. “Snakemake - A scalable bioinformatics workflow engine”. Bioinformatics 2012.
User guide and reference¶
- 1. Getting started
- 2. SnakeChunks library
- 3. Dependencies
- 4. Tutorials
- 5. Virtual environments
- 6. Snakemake
- 6.1. Introduction
- 6.2. Downloads for practical exercises
- 6.3. Demo workflows
- 6.3.1. Workflow 1: Rules and targets
- 6.3.2. Workflow 2: Introducing wildcards
- 6.3.3. Workflow 3: Keywords
- 6.3.4. Workflow 4: Combining rules
- 6.3.5. Workflow 5: Configuration file
- 6.3.6. Workflow 6: Separated files
- 6.3.7. Workflow 7: The keyword Ruleorder todo
- 6.3.8. Workflow 8: Combining wildcards with zip
- 6.3.9. Workflow 9: Combining wildcards selectively
- 6.3.10. Workflow 10: Using regular expression in wildcards
- 6.3.11. Other
- 6.4. Bonus: generating flowcharts
- 6.5. More on snakemake…
- 7. Wiki NGS & Bioinformatics