vigeas

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.

INSTALLATION

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

USAGE

Usage: 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/mamba dependencies
  version  Show last update information

CITATION

CONTRIBUTIONS

Thanks to:

• Ricardo Khouri (Rkhour0) for mentorship and discussions on improving in the -x amp and -x ill workflows.
• Verity Hill (ViralVerity) for her collaborative troubleshooting regarding low-coverage sequencing issues, primer trimming, and bioinformatic pipeline optimizations for DENV, ZIKV, and CHIKV data.

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