6. Outputs

Overview

Below is an overview of the standard outputs produced by EPITOME:

${outdir}
└── ${taxon}
    ├── ${segment}
    │   ├── ${taxon}-${segment}.summary_full.csv
    │   ├── ${taxon}-${segment}.summary_simple.csv
    │   ├── ${taxon}-${segment}.summary_taxon.csv
    │   ├── alignments
    │   │   └── ${taxon}-${segment}-${cluster}.mafft.fa
    │   ├── clusters
    │   │   ├── ${taxon}-${segment}-${cluster}.clusters.csv
    │   │   └── main_[0-9]+.png
    │   ├── consensus
    │   │   └── ${taxon}-${segment}-${cluster}.fa.gz
    │   └── qc
    │       ├── ${taxon}-${segment}.qc.csv
    │       └── ${taxon}-${segment}.qc.fa.gz
    └── ncbi-data
        ├── genomic.fa.gz
        ├── ncbi-meta.complete.csv
        ├── ncbi-meta.report-only.csv
        └── ncbi-meta.subtype-only.csv

Note

I recognize that many of these outputs would be better represented in JSON format. This is something that I hope to include in future versions. Help is always welcomed!

Summary Files

EPITOME creates multiple summaries that contain varying levels of detail:

    ├── ${segment}
    │   ├── ${taxon}-${segment}.summary_full.csv
    │   ├── ${taxon}-${segment}.summary_simple.csv
    │   ├── ${taxon}-${segment}.summary_taxon.csv

Cluster Files

Files related to sequence clustering can be found in the cluster directory. This includes plots (e.g., main_1.png) that help you visualize how clusters were created. These plots may not be produced if --max_cluster is too large.

    │   ├── clusters
    │   │   ├── ${taxon}-${segment}-${cluster}.clusters.csv
    │   │   └── main_[0-9]+.png

Reference Files

The final references are saved in the consensus directory.

    │   ├── consensus
    │   │   └── ${taxon}-${segment}-${cluster}.fa.gz

Quality Control Files

Files related to quality control of the input sequences can be found in the qc directory. You can also find a list of the QC'd sequences that were used to create the references.

    │   └── qc
    │       ├── ${taxon}-${segment}.qc.csv
    │       └── ${taxon}-${segment}.qc.fa.gz

NCBI Data

Data automatically downloaded from NCBI is saved to the ncbi-data directory. This can be useful when you need to make modifications to the reference set (can be supplied in the metadata column with --ncbi false). ncbi-meta.complete.csv is the combined versions of ncbi-meta.report-only.csv and ncbi-meta.subtype-only.csv.

    └── ncbi-data
        ├── genomic.fa.gz
        ├── ncbi-meta.complete.csv
        ├── ncbi-meta.report-only.csv
        └── ncbi-meta.subtype-only.csv