6. Outputs

Overview

Below is an overview of the standard outputs produced by EPITOME. . └── ${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