RUNNING of NF-CORE/VIRAL RECON with custom primers, reference sequence and bed files

Ask for help
,
1

Good morning, dear community,

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.

King regards

Joel Chuquimia

2

Hi @Joel_Ch_V,

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.

Phil