Data sources and preprocessing

GenSpectrum uses mostly open data from the International Nucleotide Sequence Database Collaboration (INSDC) which consists of GenBank , ENA and DDBJ .

• For influenza and RSV, we download the data directly from GenBank using the NCBI Datasets CLI. You can explore the data in our Loculus instance .
• For SARS-CoV-2, we download the data from Nextstrain who gets the data from GenBank and processes them. (For CoV-Spectrum , we have an instance which uses data from GISAID .)
• For the West Nile virus and Mpox, we use data from Pathoplexus , which also includes data from INSDC.

We use Nextclade as the main tool for preprocessing the sequences. The following sequences are used as a reference for alignment:

• SARS-CoV-2: NC_045512
• Mpox: NC_063383.1
• RSV-A: EPI_ISL_412866 (available on GISAID ; an almost identical sequences is LR699737 )
• RSV-B: OP975389.1
• West Nile virus: NC_009942.1
• Influenza A/H5N1: A/goose/Guangdong/1/1996
• Influenza A/H1N1pdm: We use the reference assembly GCF_001343785.1 except for HA (uses CY121680.1 ) and NA (uses MW626056.1).
• Influenza A/H3N2: We use the reference assembly GCF_000865085.1 except for HA (uses CY163680.1 ) and NA (uses CY114383.1).
• Influenza B/Victoria: We use the same references as the official nextclade dataset. These are:
  • seg1: CY115157.1
  • seg2: CY115158.1
  • seg3: CY115156.1
  • seg4: KX058884.1
  • seg5: CY115154.1
  • seg6: CY073894.1
  • seg7: CY115152.1
  • seg8: CY115155.1