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

Linux

git clone --recursive https://github.com/khourious/vigeas.git
cd vigeas
chmod -R +x INSTALL_Unix scripts
bash INSTALL_Unix

macOS

git clone --recursive https://github.com/khourious/vigeas.git
cd vigeas
chmod -R +x INSTALL_macOS
bash INSTALL_macOS

exec zsh

INPUT DATA FORMATS

Oxford Nanopore Technologies

POD5 is the current raw data format generated by ONT sequencing devices. For basecalling and demultiplexing, we provide an IPython notebook that utilizes GPU acceleration for faster processing, which can be used as an alternative if you don't have access to local GPU resources.

For older raw FAST5 data, ONT provides a tool to convert FAST5 files to POD5: https://pod5.nanoporetech.com/

This workflow expects demultiplexed data in BAM format. Ensure your input folder contains BAM files named with their respective barcodes (e.g., barcode01.bam, barcode02.bam). If your data is in FASTQ format, use the following conversion:

samtools import -0 input.fastq.gz -o output.bam

Prepare a sample sheet in CSV format with the following columns:

• sample_id: sample identifier
• barcode: barcode ID in BC format (e.g., BC01, BC02)
• primer_scheme: primer scheme name including version (e.g., ChikAsianECSA_V1)

Example:

976530,BC01,ARTIC_V4
985322,BC02,ZikaAsian_V2

Check available primer schemes and their correct naming format using vigeas primers or in primer_schemes/README.md.

Illumina (amplicon-based libraries)

This workflow expects demultiplexed data in FASTQ format. Both paired-end and single-end reads are supported.

Prepare a sample sheet in CSV format with the following columns:

• sample_id: sample identifier
• primer_scheme: primer scheme name including version (e.g., ChikAsianECSA_V1)

Example:

976530,ARTIC_V4
985322,ZikaAsian_V2

For multiplex amplicon schemes (e.g., OROV, Lassa), the pipeline automatically detects and processes individual segments. Simply provide the base primer scheme name in the sample sheet. Check available primer schemes and their correct naming format using vigeas primers or in primer_schemes/README.md.

Illumina (hybrid-capture-based libraries)

This workflow expects demultiplexed data in FASTQ format. Both paired-end and single-end reads are supported.

Prepare a sample sheet in CSV format with the following columns:

• sample_id: sample identifier
• panel_id: panel name (e.g., RVOP)

Example:

976530,RVOP
985322,VSP2

Check available panels and their correct naming format using vigeas panels.

USAGE

Usage: vigeas <command> or <miscellaneous>

Commands:
  ill   For Illumina Sequencing [*.fastQ data]
  ont   For ONT Sequencing [*.pod5 data]

Miscellaneous:
  bed      Generate BED file containing primer coordinates and sequences from primer scheme
  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

• Aguilar Ticona, J. P., Amorim Santos, L., Meng, X., Nery, N., Fofana, M. O., De Moraes, L., Morais Strobel, I., Vitoriano, R., Silveira Cucco, M., Andrade Belitardo, E. M. M., Thakku, G., Cruz, J. S., Detweiler, A. M., Neff, N., Tato, C. M., Reis, M. G., Costa, F., Cummings, D. A. T., Ko, A. I., & Khouri, R. (2026). Metagenomic surveillance reveals off-season circulation of respiratory viruses during the COVID-19 pandemic in Salvador, Brazil. New Microbes and New Infections, 70, 101717. https://doi.org/10.1016/j.nmni.2026.101717

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.