SCORPIO：用于定义和分类病毒基因组突变星座的实用程序。

IF 4.4 3区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Bioinformatics Pub Date : 2023-10-03 DOI:10.1093/bioinformatics/btad575

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

{"title":"SCORPIO：用于定义和分类病毒基因组突变星座的实用程序。","authors":"Rachel Colquhoun, Ben Jackson, Áine O'Toole, Andrew Rambaut","doi":"10.1093/bioinformatics/btad575","DOIUrl":null,"url":null,"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.","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":null,"pages":null},"PeriodicalIF":4.4000,"publicationDate":"2023-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10563142/pdf/","citationCount":"0","resultStr":"{\"title\":\"SCORPIO: a utility for defining and classifying mutation constellations of virus genomes.\",\"authors\":\"Rachel Colquhoun, Ben Jackson, Áine O'Toole, Andrew Rambaut\",\"doi\":\"10.1093/bioinformatics/btad575\",\"DOIUrl\":null,\"url\":null,\"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.\",\"PeriodicalId\":8903,\"journal\":{\"name\":\"Bioinformatics\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":4.4000,\"publicationDate\":\"2023-10-03\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10563142/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Bioinformatics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/bioinformatics/btad575\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/bioinformatics/btad575","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}

引用次数: 0

摘要

摘要：Scorpio提供了一套命令行实用程序，用于对一组对齐的基因组序列进行分类、单倍型和定义突变星座。它的开发是为了探索和分类SARS-CoV-2大流行中的变异毒株，但可以更广泛地应用于其他物种。可用性和实现：Scorpio是一个以GNU GPL第3版许可证分发的开源项目。源代码和二进制文件可在https://github.com/cov-lineages/scorpio和二进制文件也可从Bioconda获得。严重急性呼吸系统综合征冠状病毒2型的特定定义可以作为单独的依赖项安装https://github.com/cov-lineages/constellations.

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

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

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.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Bioinformatics 生物-生化研究方法

CiteScore

11.20

自引率

5.20%

发文量

753

审稿时长

2.1 months

期刊介绍： The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments.