I tried build custom dataset norovirus following the tutorials from https://github.com/nextstrain/nextclade_data/blob/master/docs/dataset-creation-guide.md., when creating a reference tree using Snakefile, not just described “The workflow can be configured to work with viruses other than Zika by changing the constants (in particular REFERENCE_ACCESSION, TAXON_ID, and GENES) at the top of the Snakefile.“ The resources/refrence.gb file also needs to be modified here because I found that the GB file I downloaded from NCBI is not working directly.
So could you guys tell me how to modify this GB file correctly?
I need to take a closer look at the dataset-creation-guide.md documentation, but I do have some configuration files for a Norovirus Nextclade dataset — including reference.gb files, which you can find here:
The key thing about Norovirus is that it uses a dual-gene typing system based on the VP1 and RdRp regions, so the resources/reference.gb needs to be trimmed to cover one or the other gene region for each Nextclade dataset. Hopefully these files are helpful, or let us know what errors you’re running into.
to generate Nextclade compliant gb, gff3, and fasta files. You provide an accession of an annotated reference on genbank, and the script will prompt you with a few questions, and then hopefully output a working annotation.
Thank you very much. I got the desired files Nextclade compliant gb, gff3, and fasta files for norovirus by running that scripts. But I got tree.json file like this through the command nextstrain build . test.
I am not sure, maybe there are some problems about the file pathogen.json. Because I used the value of schema same as Zika virus in example. I didn’t modify the value of schema.
The tree.json files for VP1 and RdRp are located in the nextclade_data folder. We separate the Nextclade workflow for generating the tree.json and dataset (nextclade) from our draft Nextclade dataset (nextclade_data, which contains tree.json)
Just checking, but did you want to change the title of the tree.json? From the example workflow, can adjust it in the example-workflow/resources/auspice_config.json
