SCORPIO: a utility for defining and classifying mutation constellations of virus genomes

Rachel Colquhoun; Ben Jackson; Áine O'Toole; Andrew Rambaut

doi:10.1093/bioinformatics/btad575

SCORPIO: a utility for defining and classifying mutation constellations of virus genomes

Rachel Colquhoun^*, Ben Jackson, Áine O'Toole, Andrew Rambaut

^*Corresponding author for this work

School of Biological Sciences

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English
Article number	btad575
Number of pages	4
Journal	Bioinformatics
Volume	39
Issue number	10
Early online date	15 Sept 2023
DOIs	https://doi.org/10.1093/bioinformatics/btad575
Publication status	Published - 1 Oct 2023

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10.1093/bioinformatics/btad575Licence: Creative Commons: Attribution (CC-BY)

btad575Accepted author manuscript, 280 KBLicence: Creative Commons: Attribution (CC-BY)

The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control
Rambaut, A.
EU government bodies
1/08/17 → 31/07/23
Project: Research
Putting genomic surveillance at the heart of viral epidemic response.
Rambaut, A.
UK-based charities
1/08/17 → 31/07/24
Project: Research

Cite this

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title = "SCORPIO: a utility for defining and classifying mutation constellations of virus genomes",

abstract = "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.",

author = "Rachel Colquhoun and Ben Jackson and {\'A}ine O'Toole and Andrew Rambaut",

note = "Funding Information: This work was supported by Wellcome Trust [Collaborators Award 206298/Z/17/Z ARTIC network]; the European Research Council [725422—ReservoirDOCS]; and Medical Research Council (MRC) [MC_PC_19027—COG-UK]. Publisher Copyright: {\textcopyright} The Author(s) 2023. Published by Oxford University Press.",

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doi = "10.1093/bioinformatics/btad575",

language = "English",

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T1 - SCORPIO: a utility for defining and classifying mutation constellations of virus genomes

AU - Colquhoun, Rachel

AU - Jackson, Ben

AU - O'Toole, Áine

AU - Rambaut, Andrew

N1 - Funding Information: This work was supported by Wellcome Trust [Collaborators Award 206298/Z/17/Z ARTIC network]; the European Research Council [725422—ReservoirDOCS]; and Medical Research Council (MRC) [MC_PC_19027—COG-UK]. Publisher Copyright: © The Author(s) 2023. Published by Oxford University Press.

PY - 2023/10/1

Y1 - 2023/10/1

N2 - 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.

AB - 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.

U2 - 10.1093/bioinformatics/btad575

DO - 10.1093/bioinformatics/btad575

M3 - Article

C2 - 37713452

SN - 1367-4803

VL - 39

JO - Bioinformatics

JF - Bioinformatics

IS - 10

M1 - btad575

ER -

SCORPIO: a utility for defining and classifying mutation constellations of virus genomes

Abstract

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Projects

The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control

Putting genomic surveillance at the heart of viral epidemic response.

Cite this