VIral GEnome ASsembly pipelines for WGS

This repository contains scripts and files to run the bioinformatic analysis of whole genome sequencing of viruses using Illumina or Oxford Nanopore Technologies platforms.

Usage:   vigeas <command> [options]

Commands:
  -- ILLUMINA ASSEMBLY
       dnap     For libraries using Illumina DNA Prep or similar [*.fastQ data]
       rnapenr  For libraries using Illumina RNA Prep with Enrichment or similar [*.fastQ data]

  -- OXFORD NANOPORE TECHNOLOGIES ASSEMBLY
       ont      For libraries using ONT SQK-LSK109 or similar [*.fast5/*.pod5 data]

  -- Misc
       update   Update conda [micromamba] dependencies
       panels   List available enrichment panels in this workflow -- for <vigeas rnapenr>
       primers  List available primer schemes in this workflow -- for <vigeas dnap> and <vigeas ont>

Setting up the pipeline

Download and install the pipeline from the github repo:

git clone --recursive https://github.com/khourious/vigeas.git; cd vigeas
chmod 700 -R INSTALL
bash INSTALL