CoV-Seq, a New Tool for SARS-CoV-2 Genome Analysis and Visualization: Development and Usability Study (Preprint)

Abstract

<sec> <title>BACKGROUND</title> <p>COVID-19 has become a global pandemic not long after its inception in late 2019. SARS-CoV-2 genomes are being sequenced and shared on public repositories at a fast pace. To keep up with these updates, scientists need to frequently refresh and reclean datasets, which is ad hoc and labor-intensive. Further, scientists with limited bioinformatics or programming knowledge may find it difficult to analyze SARS-CoV-2 genomes.</p> </sec> <sec> <title>OBJECTIVE</title> <p>To address these challenges, we developed CoV-Seq, an integrated webserver to enable simple and rapid analysis of SARS-CoV-2 genomes.</p> </sec> <sec> <title>METHODS</title> <p>Given a new sequence, CoV-Seq automatically predicts gene boundaries and identifies genetic variants, which are displayed in an interactive genome visualizer and are downloadable for further analysis. A command-line interface is also available for high-throughput processing. Also, we aggregate all publicly available SARS-CoV-2 sequences from GISAID, NCBI, ENA, and CNGB, and extract genetic variants from these sequences for download and downstream analysis. The CoV-Seq database is updated weekly.</p> </sec> <sec> <title>RESULTS</title> <p>CoV-Seq is implemented in Python and Javascript. The web server is available at http://covseq.baidu.com/ and the source code is available from https://github.com/boxiangliu/covseq.</p> </sec> <sec> <title>CONCLUSIONS</title> <p>We have developed CoV-Seq, an integrated web service for fast and easy analysis of custom SARS-CoV-2 sequences. The web server provides an interactive module for the analysis of custom sequences and weekly updated database of genetic variants from all publicly accessible SARS-CoV-2 sequences. We hope CoV-Seq will help improve our understanding of the genetic underpinnings of COVID-19.</p> </sec>