Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.08.330456v1?rss=1 Authors: Zhu, X., Chang, T.-C., Webby, R., Wu, G. Abstract: idCOV is a phylogenetic pipeline for quickly identifying the clades of SARS-CoV-2 virus isolates from raw sequencing data based on a selected clade-defining marker list. Using a public dataset, we show that idCOV can make equivalent calls as annotated by Nextstrain.org on all three common clade systems using user uploaded FastQ files directly. Web and equivalent command-line interfac-es are available. It can be deployed on any Linux environment, including personal computer, HPC and the cloud. The source code is available at https://github.com/xz-stjude/idcov. A documentation for installation can be found at https://github.com/xz-stjude/idcov/blob/master/README.md. Copy rights belong to original authors. Visit the link for more info