3. Preparing Inputs

Overview

EPITOME has several built-in features that help you source and manage your input data. You can also supply data manually with or without these automated features. Keep on scrolling to learn more!

Data Sources & Formatting

Sourcing data from public repositories can be challenging and is often messy and sometime unreliable. EPITOME attempts to automate this process 😅. You can also skip this all together and supply your data manually (can also be combined with the automated process!). In either case, all data is eventually combined per taxon and run through some basic quality control steps before being passed on for reference creation.

Automated Data Sourcing

EPITOME can automatically download complete sequences for a specified taxon from NCBI. This feature is controlled using the --ncbi parameter (default: --ncbi true. When enabled, EPITOME will pull all complete sequences for each taxon name in your samplesheet. This is accomplished using the NCBI datasets virus package.

But wait, there's more...

The sample data supplied with sequences downloaded using datasets download virus genome taxon is currently lacking. Specifically, we are often missing crucial information such as segment information or taxonomic details, such as the species name or reported subtype (e.g., H5N1). This additional info is gathered using the taxonomy package from NCBI datasets, combined with an esearch of the NCBI nucleotide database using the following query: ${taxon}[Organism] AND "complete sequence"[Title]. These datastreams are then combined into a single table.

Note

Taxon names must match the taxId used by NCBI (learn more here).

Supplying Data Manually

Data can also be supplied manually for a taxon via the samplesheet. Sequence data is supplied as a multi-fasta file via the assembly column and sequence sample data is supplied as a CSV file via the metadata column. Below is an example samplesheet and metadata file:

samplesheet.csv:

taxon,assembly,metadata,segmented
Betacoronavirus,betacoronavirus.fa.gz,betacoronavirus.meta.csv,FALSE

betacoronavirus.meta.csv

"accession","species"
"JX993988.1","Severe acute respiratory syndrome-related coronavirus"

Note

The only information required in the sample data file is the accession column and the segment column, if the virus has a segmented genome. Otherwise, you are free to supply as much/little info as you like, using whatever column names you like (there are probably some limitations - let me know when you find them! 😄).

 

Input QC