VirFinder_ensemble_training

Scripts for training of an ensemble of linear classifiers using VirFinder This pipeline is meant to be run on an HPC with a PBS scheduler.

Quick start

Prerequisites

You need to have the R package VirFinder and its dependencies installed.

Edit the config.sh file

please modify the

• V_DATASET = indicate here the fasta file containing viral sequences for the training set
• H_DATASET = indicate here the fasta file containing host sequences for the training set
• RESULT_DIR = indicate here the directory for the outputs
• SPLIT_SIZE = indicate the number of training example to train the models on
• ENS_SIZE= indicate the number of models to train
• KM_SIZE= indicate the kmer size to use for the training
• MAIL_USER = indicate here your arizona.edu email
• GROUP = indicate here your group affiliation

Run ./submit

this command will submit two jobs in queue.