This repository contains files to enable the use of the 18SNemaBase database for the wf-metagenomics workflow in EPI2ME. N.B. we have updated the 18S_NemaBase.fasta file to use underscores in place of any spaces in the reference names to ensure proper mappings.
The required files are created using the create_ref2taxid.jl script. This takes the reference list from 18SNemaBase (18S_NemaBase.fasta) and generates the ref2taxid_18S_NemaBase.txt file that maps the species of each reference to a valid taxids in NCBI. This is possible by using the taxid2name.txt file that was taken from a taxonomy dump from the NCBI. Any references (i.e., species) not present in the NCBI mapping will be given the taxid 28384 ("other sequence").
To use this database in the wf-metagenomics EPI2ME workflow, you need to select the minimap2 aligner, use the 18S_NemaBase.fasta file as the reference library and ref2taxid_18S_NemaBase.txt for the ref2taxid mapping option.
For further information on how to use a custom database with the wf-metagenomics workflow see the documentation at: https://labs.epi2me.io/metagenomic-databases/