Simulated NGS read datasets for novel human virus prediction

This repository contains simulated Illumina read datasets for novel human virus prediction and associated metadata extracted from the Virus Host Database (https://www.genome.jp/virushostdb/). The reads are 250bp long and were simulated with Mason (https://www.seqan.de/apps/mason/) from genomes downloaded from NCBI. The training-validation-test split was done on whole viral sequences to ensure "novelty" of validation and test viruses. The training sets contain 10 million reads per class, validation sets - 1.25 million reads per class, and test sets - 1.25 million paired reads per class. The negative class sets contain reads simulated from chordate-infecting ("cho"), metazoan-infecting ("met"), eukariote-infecting ("euk") and all-nonhuman viruses. The positive class contains human-infecting viruses. The stratified dataset ("strat") contains an equal number of reads from "cho", "met but not cho", "euk but not met" and "all but not euk". 

Species-level datasets ("humspec", "allspec" and "chospec", with the corresponding fasta and *_species.rds files) are constructed analogously, but ensuring that all viruses of a given species were assigned to either training, val or test set. This is a stricter setting modelling a "novel viral species" scenario while reflecting within-species phenotype diversity.

blast_hits.gz contains blast hits of human virome reads form Moustafa et al., 2017 (https://doi.org/10.1371/journal.ppat.1006292) blasted against our training database (see paper for details). In the second column you can find the matched label and the accession number of the matched reference. blast_labels_complete.gz contains extracted labels for all virome reads, including those without any matches. Note: one of the read headers (>3c8ac47039d32b11c8fe23f588e444e9) from Moustafa et al. is slightly corrupted with null characters. You can remove them with sed 's/\x0//g' or equivalent.