I have sequenced the complete genome of the dengue virus using nanopore technology. I understand that the viralrecon pipeline is a good option to analyze nanopore data, especially for assembly, but this pipeline, according to its characteristics, supports analysis based on amplicons obtained from primer sets created and maintained by the ARTIC network. In my case, the sequencing I performed was with custom primers with their respective reference sequences and bed files. My question is, is there any possibility of adapting this pipeline with my primers, reference sequences and bed using nextflow so that I can assemble my dengue nanopore data? Clearly the primers I used for sequencing are not in the ARTIC network.
I don’t know if anyone tried to modify or adapt this pipeline, because the truth is that there are not many pipelines that analyze (especially assemble) nanopore data that are freely accessible, for example, there is genome detective but it is paid.
nf-core/viralrecon was indeed originally written for SARS-Cov2, but it was designed in a way to make it flexible for any viral analysis. It’s definitely been used for plenty of others, for example it has out of the box support for Monkeypox as well. But it can work with anything as long as you have the relevant reference and primers.
I would have a look at the parameters page to see the different inputs to the pipeline:
For more help, please join the nf-core Slack organisation (Join nf-core) and see the channel called #viralrecon.
There’s nothing for me to look into @Rohit-Satyam - the answer was yes, the pipeline can be run for any other virus / organism.
Depending on how exactly you run the pipeline, you probably will need the primers though, these are required for the analysis.
There are several supported by the pipeline out of the box (SARS-CoV2, Monkeypox, HIV, see the relevant pipeline config file) and it would be great to collaborate and add more primer sets to the pipeline for other users.
If you need help with the pipeline, please join the nf-core slack as mentioned above.
For assembly Whole genome of virus by ONT, you can use another platform based on mapping to referencing instead of artic even you already using pcr amplicon approach.