viralrecon is conceived as a target viral reconstrucion pipeline. The de novo assembly is not ment for multiple virus assembly, but rather a complex virus assembly, such as enterovirus, or some hepatitis. The idea is that the pipeline serves to reconstruct all possible target virus, HIV, Enterovirus, SARS-CoV-2, MPXV, Crimea Congo, Hantavirus, without the need of using 15 different pipelines for each virus. That includes the resistance detection approaches, for HIV or influenza in the future.

And with target I don't mean amplification, but rather that you only expect one virus in the sample

That said, I identify 2 different pipelines, as it is in the tube map: 1. Mapping against reference (+ resistance in HIV) (for Illumina and nanopore) 2. De novo assembly (for illumina)

We can adapt to whatever the community wants, in case they prefer to have different pipelines for each virus, we can continue to integrate the other virus in our own fork. But the HIV resistance detection was included as the community asked for it to have an all-in-one pipeline for target viral reconstruction

In the future plans we have the idea to include IRMA's CDC to reconstruc influenza and RSV, and also include the influenza resistance detection.

But if the community does not want it in viralrecon, we can do it in our own fork of viralrecon

We discuss this in the montly meetings if you want to join!

Which timezone are the monthly meetings?

UTC+2?

This week I won't be able to join as I'll be in a workshop in switzerland, but I'll let you know for the next one if you want to join!

Having said that, I still think HIV and wastewater should form their own separate pipeline. But I don't want to divide the community! So I'll look into how I can start contributing to viralrecon to suit my organisations needs.