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Somatem is a nextflow pipeline purpose built for the processing of long-read genomic sequencing data. Somatem is built from nextflow with a modular design, enabling additions and updates to be added to the subworkflows without having to rewrite the whole pipeline. A brief overview is outlined in this slide deck
Somatem currently has 4 major subworkflows:
- 16S taxonomic profiling
- Metagenomic taxonomic profiling
- Metagenome-assembled genome (MAG) construction
- Longitudinal bacterial dynamics (temporal SV analysis)
The inner workings of each subworkflow will be included in their respective wiki links to the right, including usage and examples of how to run each pipeline.