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Fig. 1 | BMC Bioinformatics

Fig. 1

From: VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank

Fig. 1

Example usage of VAPiD. The two required files are shown as genome.fasta and author_info.sbt. Genome.fasta is all of the viral genomes you wish to submit, named as you want them to appear on GenBank. In the example code provided in the github repository this example file is called example.fasta. The author_info.sbt file is an NCBI specific file for attaching sequence author names to sequin files and is a required part of properly submitting sequences to NCBI. This file can be generated at (https://submit.ncbi.nlm.nih.gov/genbank/template/submission/ ). The first optional command is a comma separated file in which you can include all relevant metadata. You can create additional columns here so long as they correspond to NCBI approved sequence metadata. A list and formatting requirements can be found at (https://www.ncbi.nlm.nih.gov/Sequin/modifiers.html). Note that FASTA sequence names must be identical to names in the optional metadata sheet. Additionally, one could omit the metadata sheet and VAPiD will prompt for strain name, collection-date, country, and coverage data automatically at runtime. The second optional argument is a location of a local BLASTn database, which will force VAPiD to use the specified database instead of the included database. The last optional argument will force VAPiD to send an online search query to NCBI’s NT database

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