Metrics

Input assembly metrics

• Can be found in input_assemblies.yaml (one file for each assembly).
• Created when running Autocycler compress.

Clustering metrics

• Can be found in clustering/clustering.yaml (one file for each assembly).
• Created when running Autocycler cluster.

Untrimmed cluster metrics

• Can be found in clustering/qc*/cluster_*/1_untrimmed.yaml (one file for each cluster).
• Created when running Autocycler cluster.

Trimmed cluster metrics

• Can be found in clustering/qc*/cluster_*/2_trimmed.yaml (one file for each cluster).
• Created when running Autocycler trim.

Consensus assembly metrics

• Can be found in consensus_assembly.yaml (one file for each assembly).
• Created when running Autocycler combine.