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bioRxiv · 10.1101/2020.10.08.330456

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

Zhu, X.·Chang, T.-C.·Webby, R.·Wu, G.
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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 interfaces 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.

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Zhu, X., Chang, T.-C., Webby, R., Wu, G.. 2020-10-09. idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates. https://doi.org/10.1101/2020.10.08.330456

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