ViReaDB: A user-friendly database for compactly storing viral sequence data and rapidly computing consensus genome sequences

Motivation

In viral molecular epidemiology, reconstruction of consensus genomes from sequence data is critical for tracking mutations and variants of concern. However, storage of the raw sequence data can become prohibitively large, and computing consensus genome from sequence data can be slow and requires bioinformatics expertise.

Results

ViReaDB is a user-friendly database system for compactly storing viral sequence data and rapidly computing consensus genome sequences. From a dataset of 1 million trimmed mapped SARS-CoV-2 reads, it is able to compute the base counts and the consensus genome in 16 minutes, store the reads alongside the base counts and consensus in 50 MB, and optionally store just the base counts and consensus (without the reads) in 300 KB.

Availability

ViReaDB is freely available on PyPI (https://pypi.org/project/vireadb) and on GitHub (https://github.com/niemasd/ViReaDB) as an open-source Python software project.