SUMMARY: 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 https://github.com/cov-lineages/scorpio, and binaries are also available from Bioconda. SARS-CoV-2 specific definitions can be installed as a separate dependency from https://github.com/cov-lineages/constellations.


This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Cite as

Jackson, B., O'Toole, Á., Rambaut, A. & Colquhoun, R. 2023, 'SCORPIO: a utility for defining and classifying mutation constellations of virus genomes', Bioinformatics, 39(10), article no: btad575. https://doi.org/10.1093/bioinformatics/btad575

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Last updated: 11 October 2023
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