Reference Dataset

Help and Getting Started
1

Hello.

I have been using Nextclade web to analyze my RSV data. I usually used the reference listed in the metadata, which I downloaded from auspice web. I noticed there is a change in the accession listed in the metadata. For example, RSV lineage A from north America (1956-XX-XX, by Wang,L.,Ng,T.F.F.,Castro,C.J.,Marine,R.L.,Magana,L.C.,Esona,M.,Peret,T.C.T.,Thornburg,N.J.) had “OK649668” as the accession ID in the past, but now I see a new accession number “PP_001NQRF”.

I tried to use PP_001NQRF in GenBank, EMBL, and INSDC but it did not work. On this page Nextclade datasets — Nextclade documentation “Nextclade Web loads the latest compatible datasets automatically. User can choose one of the datasets before starting the analysis using the dataset selector. The datasets page displays all the available datasets and allows to download them. These downloaded datasets can be used with Nextclade Web in advanced mode or with Nextclade CLI. They can also serve as a starting point for creating your own datasets.”

When I opened the GitHub page on RSV-A, I could not find the accession numbers based on the metadata from auspice and vice versa. In the past I could simply use the accession listed and search in GenBank.

I am kind of lost now; can someone please guide me to where I can download the references used in Nextclade?

Thank you

2

Hello @eli_rdp,

I missed that you had posted on the discussion board, so posting my response here as well for others who might have the same question:

The data source for RSV has recently changed from NCBI Genbank to Pathoplexus, so the “PP_” accessions are the Pathoplexus accessions.

You can browse and search for RSV lineage A sequences at https://pathoplexus.org/rsv-a/

Best,
Jover

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