An improved downloaded function for GISAID is planned for the next update. For now, please use the following workaround:

  • Step 1: Download the selected sequences from GISAID as multiple fasta file.
  • Step 2: Invoke the SeqSphere menu function Tools | Other Utilities | Split Multiple FASTA file into FASTA files and choose the downloaded file. In the dialog choose a empty directory for storing the files.
  • Step 3: Create a new SARS-CoV-2 pipeline. In the "Define Input Sources" section, select the directory where the split FASTA files were stored. Press the button "Advanced Input Source Options". Then enable the checkbox Use Regular Expressions and type in field right of it the regular expression
(EPI_ISL_\d+)


The pipeline can then be started to import all split sequences. After the samples are processed, the metadata downloaded from GISAID can be imported. The matching of GISAID fields to SeqSphere fields is currently not automatically supported, i.e., some GISAID fields (e.g. location, patient age) must be mapped manually to SeqSphere fields.