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EPITOME: Enhanced Phylogenetic Inference Through Optimized Mapping Efficiency

EPITOME condenses a diverse set of DNA sequences into discrete, composite sequences that represent the overarching diversity of the dataset. In other words, EPITOME creates sequences that are the epitome of the dataset diversity. This is accomplished by clustering the input based on pairwise genetic distances and then selecting the most common nucleotide at each genomic position (ties selected at random). When the genetic distance is based on read mapping efficiency, EPITOME creates a set of reference genomes for consensus-based assembly pipelines, like VAPER.

See the wiki for more information.

Quick Start

Step 1. Create your samplesheet

Note

The example below creates a reference set for each taxon using data automatically downloaded from NCBI. It is also possible to supply your own sequence data with or without the NCBI data - learn more here.

samplesheet.csv:

taxon,segmented,segmentSynonyms
Hantavirus,TRUE,s|small;m|medium|middle;l|large
Norovirus,FALSE,

Step 2. Run EPITOME

Run EPITOME using the command below.

nextflow run DOH-JDJ0303/epitome \
    -r main \
    -profile docker \
    --input samplesheet.csv \
    --outdir results