Faster SARS-CoV-2 sequence validation and annotation for GenBank using VADR.

ABSTRACT:

Background

In 2020 and 2021, more than 1.5 million SARS-CoV-2 sequences were submitted to GenBank. The initial version (v1.0) of the VADR (Viral Annotation DefineR) software package that GenBank uses to automatically validate and annotate incoming viral sequences is too slow and memory intensive to process many thousands of SARS-CoV-2 sequences in a reasonable amount of time. Additionally, long stretches of ambiguous N nucleotides, which are common in many SARS-CoV-2 sequences, prevent VADR from accurate validation and annotation.

Results

VADR has been updated to more accurately and rapidly annotate SARS-CoV-2 sequences. Stretches of consecutive Ns are now identified and temporarily replaced with expected nucleotides to facilitate processing, and the slowest steps have been

SUBMITTER: Nawrocki EP 

PROVIDER: S-EPMC9094095 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature