Hello All, I have been running viralrecon for a previous library prep method for West Nile virus with success but I have switched prep kits to a single tube multiplex reaction calleg xGen from IDT that allows for varying lengths of amplicons. Would there be an easy way to modify the viralrecon pipeline to account for the single tube reaction? I currently get errors because there is not a LEFT RIGHT indication in the .bed file. They are formatted in the .bed file attached. I also attached the pipeline that currently exists that was shared with me. It works but it is not set up to run samples in parallel and would prefer a nextflow solution. If it isn’t viralrecon perhaps another nf-core pipeline suggestion

So the amplicon scheme has primers inside of primers? eg

_______________________________________ REF
    ->                             <-   Primer 1
         ->           <-                Primer 2

As Ammar said, you can either add the

_LEFT

and

_RIGHT

suffix to your bed file, or you can change these params: https://nf-co.re/viralrecon/3.0.0/parameters/#primer_left_suffix

--primer_left_suffix

and

--primer_right_suffix

to the one used in your bed file, like

.t1

or

.t0

if that is correct for your specific primers! Hope this helps! Let us know if it worked!