Scorpio provides a set of command line utilities for classifying, haplotyping, and defining constellations of mutations for an aligned set of genome sequences. It was developed to enable exploration and classification of variants of concern within the SARS-CoV-2 pandemic, but can be applied more generally to other species.

Availability and implementation

Scorpio is an open-source project distributed under the GNU GPL version 3 license. Source code and binaries are available at, and binaries are also available from Bioconda. SARS-CoV-2 specific definitions can be installed as a separate dependency from

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