title: Workflow overview subtitle: Complete analysis pipeline for viral metagenomics
Viralmetagenome takes in a set of reads and performs 5 major analyses, each of them are explained in more detail in the following sections:
- Preprocessing
- Metagenomic diversity
- Assembly & Polishing
- Variant analysis & iterative refinement
- Consensus evaluation
By default all analyses are run.
Skipping steps
All steps can be skipped and the pipeline can be run with only the desired steps. This can be done with the --skip_preprocessing, --skip_read_classification, --skip_assembly, --skip_polishing, --skip_variant_analysis, --skip_iterative_refinement, --skip_consensus_qc flags.
Subway map
