CoV-Seq: SARS-CoV-2 Genome Analysis and Visualization
Abstract
Summary
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. In order to address these challenges, we developed CoV-Seq, a webserver to enable simple and rapid analysis of SARS-CoV-2 genomes. Given a new sequence, CoV-Seq automatically predicts gene boundaries and identifies genetic variants, which are presented in an interactive genome visualizer and are downloadable for further analysis. A command-line interface is also available for high-throughput processing.
Availability and Implementation
CoV-Seq is implemented in Python and Javascript. The webserver is available at<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://covseq.baidu.com/">http://covseq.baidu.com/</ext-link>and the source code is available from<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/boxiangliu/covseq">https://github.com/boxiangliu/covseq</ext-link>.
Contact
<email>jollier.liu@gmail.com</email>
Supplementary information
Supplementary information are available atbioRxivonline.
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