Biological Sequence Quality Control and Organization

National Library Of Medicine

Investigators

Linked publications, trials & patents

Abstract

During the past year, we improved our software package VADR (https://github.com/nawrockie/vadr) for viral sequence annotation using models based on RefSeq annotation. VADR aligns complete input sequences to their nearest RefSeq sequence and uses that alignment to map the RefSeq annotation onto the input sequences. VADR is used by GenBank to help annotate Norovirus, Dengue virus, SARS-CoV-2 and metazoan cytochrome C oxidase subunit 1 (COX1) protein-coding gene sequences. Most of the development of VADR in the past year was aimed at facilitating and improving validation and annotation of SARS-CoV-2 sequences. In particular, we made VADR more efficient so that it could handle more than one hundred thousand sequences per month. In 2021, VADR was used to annotate and validate more than 1.5 million SARS-CoV-2 sequences submitted to GenBank. In December 2021, we released a new version of VADR (v1.4) and switched to using a single reference model based on the NC_045512 reference sequence for more consistent and easily-interpretable results. We made additional releases of the software in January 2022 (v1.4.1) and July 2022 (v1.4.1) which were both minor updates. In March 2022, a manuscript on the GenBank pipeline for automatic validation and annotation of SARS-CoV-2 sequences, which involves VADR and so is related to this project, was published in the journal Database. In July 2022, we made the first VADR monkeypox virus (MPXV) model available. It is currently used manually by GenBank curators for analyzing MPXV sequence submissions. In August 2021, a manuscript describing the Ribovore software package, which is part of this project, was published in the journal BMC Bioinformatics.