This repository contains scripts and files to run the bioinformatic analysis of whole genome sequencing of viruses using Illumina or Oxford Nanopore Technologies platforms.
git clone --recursive https://github.com/khourious/vigeas.git; cd vigeas
chmod 700 -R INSTALL
bash INSTALLUsage: vigeas <command> or <miscellaneous>
Commands:
ill For Illumina Sequencing [*.fastQ data]
ont For ONT Sequencing [*.pod5 data]
Miscellaneous:
clr3 List supported Clair3 models
makedb Create a BLAST database in this workflow -- for <vigeas ill -x hyb>
panels List available enrichment panels in this workflow -- for <vigeas ill -x hyb>
primers List available primer schemes in this workflow -- for <vigeas ill -x amp> and <vigeas ont -x bda>
update Update conda [micromamba] dependencies