Reference Viral DataBase (RVDB)

Reference Viral Database (RVDB) is developed by Arifa Khan's group at CBER, FDA for enhancing virus detection using high-throughput/next-generation sequencing (HTS/NGS) technologies. Unique features include reduction/removal of phages, misannotated, irrelevant, and non-viral sequences by manual curation. RVDB is available as Unclustered (U-) and Clustered (C-) nucleotide sequence files. The scripts and steps involved in the generation, update, and refinement of RVDB have been published ( 1, 2 ) and the assembled pipelines are available with instructions at GitHub. An automatic pipeline for non-viral annotation was implemented from U-RVDBv27.0. The Terms of use for RVDB are listed here .

The SQLite form of U-RVDB is provided using the sqlite3 module available in python, as described by GitHub. From version 15.1 and thereafter, the RVDB SQLDB is converted to SQLite to provide a flexible import format.

A proteic version of RVDB was developed by Marc Eloit’s group and is available at Institut Pasteur (RVDB-prot and RVDB-prot-HMM). The proteic RVDB may be used to complement analysis using these nucleotidic databases.