Title: Support for Using Viralrecon with Other Arboviruses (e.g., Chikungunya and Dengue)

[nascimento-jean]

Hello nf-core/viralrecon team,

First, thank you for maintaining such a robust and well-documented pipeline. Viralrecon has been extremely useful in our laboratory for viral genomic surveillance using Illumina short-read data.

I would like to ask for clarification — and possibly guidance — on how to properly adapt the pipeline for use with non–SARS-CoV-2 viruses, specifically arboviruses such as Chikungunya virus (CHIKV) and Dengue virus (DENV).

Context

I am working with clinical samples sequenced on Illumina MiSeq (paired-end), using both amplicon-based and metagenomic approaches. My goal is to use Viralrecon for:

Read QC and primer trimming

Reference-based alignment

Variant calling and consensus generation

Coverage analysis and reporting

Questions

Is Viralrecon fully compatible with non–SARS-CoV-2 genomes, such as CHIKV or DENV, when providing a custom reference FASTA?

For amplicon-based protocols:

Can we supply custom primer BED/FASTA files in place of ARTIC primer schemes?

Are there any limitations or assumptions in the current modules that are specific to SARS-CoV-2 primer sets or genome structure?

Are there recommended adjustments for variant-calling parameters when working with non-segmented viruses (like CHIKV) or segmented ones (like DENV, if applicable to future updates)?

Is there an example or documentation on running Viralrecon with other reference genomes, especially for viruses with different genome sizes, complexities, or amplicon strategies?

Feature Request

Would it be possible to include:

A generic amplicon mode, allowing any virus to be processed as long as the user provides reference + primers?

Example configuration files or templates for other viral genomes?

(If feasible) a small tutorial or documentation section explaining how to adapt the pipeline for other viruses commonly processed in public health and research laboratories (e.g., CHIKV, DENV, MAYV, OROV, etc.).

This would greatly benefit groups working with multiple emerging pathogens, especially in regions where arbovirus outbreaks are frequent.

If the team is open to it, I would be glad to assist with testing and validating the adaptation for CHIKV and DENV. We can provide datasets, reference genomes, and primer sets for benchmarking.

Thank you very much for your time and for all your work on nf-core.

Best regards,
Jean Nascimento

[svarona]

Hi Jean, thanks for reaching out! If you want a more dynamic discussion you can always write your questions in the nf-core/viralrecon slack channel. I'll try to answer your questions.

Yes, viralrecon can be used with many viruses beyond SARS-CoV-2 for Illumina Short-read data, when a suitable configuration (reference genome, primer scheme if applicable, and parameter tuning) is provided.

Although the pipeline was originally developed and is most commonly used for SARS-CoV-2 genomic surveillance, it is not limited to that virus. Internally and in collaborative projects, viralrecon has been successfully used for multiple viruses, including Rabies virus, Rubella virus, Measles virus, Mumps virus, Crimean-Congo hemorrhagic fever virus, West Nile virus, Sindbis virus, Monkeypox virus or Respiratory Syncytial Virus. Here you have some use cases where we have succesfully used it for some of these viruses:
https://pubmed.ncbi.nlm.nih.gov/38140614/
https://pubmed.ncbi.nlm.nih.gov/39760017/
https://pubmed.ncbi.nlm.nih.gov/36851481/
https://pubmed.ncbi.nlm.nih.gov/35830908/
https://pubmed.ncbi.nlm.nih.gov/38062945/

In these cases, no modifications to the pipeline code were required. The main adaptation involved adjusting pipeline parameters and providing appropriate reference genomes, primer schemes (when applicable), and variant-calling settings.

The default parameter values in viralrecon are tuned for SARS-CoV-2 workflows, so users working with other viruses should review the configuration carefully and adapt parameters accordingly.

Here you have all the params that can be changed in the pipeline:
https://nf-co.re/viralrecon/3.0.0/parameters/

I can share some examples with you, for example we have been using it for RSV primer amplification:

nextflow run nf-core-viralrecon-3.0.0 \
          --input samplesheet.csv \
          --outdir EPI_ISL_18668201_20251230_viralrecon_mapping \
          --platform 'illumina' \
          --protocol 'amplicon' \
          --kraken2_db '/reference/hg38/UCSC/kraken2/kraken2_human.tar.gz' \
          --variant_caller 'ivar' \
          --consensus_caller 'bcftools' \
          --skip_pangolin \
          --skip_freyja \
          --fasta /refrence/paramyxoviridae/fasta/EPI_ISL_18668201.fa \
          --primer_bed 'RSVWGS_18668201_scheme.bed' \
          --primer_fasta 'Primers_scheme_RSVWGS_v3.fasta' \
          --primer_left_suffix "_F" \
          --primer_right_suffix "_R" \
          --nextclade_dataset_name 'rsv_a' \
          -resume

Just remember to use the proper params for primers as indicated in the documentation.

It is really difficult to create documentation for ALL the viruses for which viralrecon can be used, as mos of it is just providing a propper .fasta and .bed files.