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
       ill-amp  For libraries using Amplicon chemistry [*.fastQ data]
       ill-hyb  For libraries using Hybrid-capture chemistry [*.fastQ data]

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

  -- Misc
       makedb   Create a BLAST database in this workflow -- for <vigeas ill-hyb>
       panels   List available enrichment panels in this workflow -- for <vigeas ill-hyb>
       primers  List available primer schemes in this workflow -- for <vigeas ill-amp> and <vigeas ont>
       update   Update conda [micromamba] dependencies

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