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

Column Descriptions

Note

EPITOME summarizes the metadata associated with each input sequence used to create a reference genome, when available. This information reported exactly as listed in NCBI when using --ncbi true (interpret with caution!).

Column	Description
TAXON	Taxonomic name used to create the reference set.
SPECIES	Species name(s) of sequences used to create the reference.
COLLECTIONDATE	Collection date range of sequences used to create the reference.
GEOGRAPHICREGION	Geographic region(s) of sequences used to create the reference.
ORGANISMNAME_HOST	Taxonomic name(s) of the host organism of sequences used to create the reference.
SEROTYPE	Serotype(s) of sequences used to create the reference.
LINEAGE	Lineage(s) of sequences used to create the reference.
CLADE	Clade(s) of sequences used to create the reference.
HA_TYPE	Influenza hemagglutinin subtype(s) (derived from SEROTYPE).
NA_TYPE	Influenza neuraminidase subtype(s) (derived from SEROTYPE).
NEIGHBOR	Name of the most closely related reference in the reference set.
NEIGHBOR_ANI	Percent average nucleotide identity of the closest related reference in the reference set.
N_RAW	Number of raw sequences used to create the reference (includes exact replicates).
N_QC	Number of quality controlled sequences used to create the reference (excludes exact replicates)

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