Version 1.2

Version 1.2 of VAPiD contains three reference viral databases. The all_virus database is all complete viral genomes on NCBI's NT as of May 1, 2018. The compressed database is this same database but CD-HIT at 95% similarity. ref_seq_vir is NCBI's viral ref_seq as of August 14th, 2018.

Viral sequences submitted after the dates listed above (2019-nCov) will NOT be present in these databases. You can add them manually to the provided fasta and then run makeblastdb -in *.fasta -dbtype nucl

The recommended database is 'all_virus.zip' - Download and unzip this to your vapid folder

but on extremely resource limited computers the compressed database should work. The ref_seq_vir database has excellent annotations but may not provide adequate breadth of sequence diversity to correctly annotate your viruses.

To run vapid all you need to download is the zip which contains (.nin, .nhr, and .nsq). The .fasta is provided so that you can add your own sequences and then remake the blast database. makeblastdb -in *.fasta -dbtype nucl

To get VAPiD working, just download one of the three sets of files (.nin .nhr .nsq) and place them in your VAPiD folder. You also need blast+ working on your computer to enjoy the fast speeds of a local search.