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6. Outputs

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Jared Johnson edited this page Feb 28, 2025 · 8 revisions

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

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