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.  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 .
idCOV
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. 
Nextstrain.org
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. 
FastQ
It can be deployed on any Linux environment, including personal computer, HPC and the cloud. 
Linux