idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates

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 interfaces are available. It can be deployed on any Linux environment, including personal computer, HPC and the cloud. The source code is available at <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/xz-stjude/idcov">https://github.com/xz-stjude/idcov</ext-link> . A documentation for installation can be found at <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/xz-stjude/idcov/blob/master/README.md">https://github.com/xz-stjude/idcov/blob/master/README.md</ext-link> .