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PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

Abstract:
Abstract Background Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Advances in whole genome sequencing technologies have led to a vast expansion in the amount of bacterial genomes deposited in public databases. There is a pressing need for software solutions which are able to cluster, catalogue and characterise genes, or other features, in increasingly large genomic datasets. Results Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement and Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software developments to allow for the rapid interrogation of thousands of isolates. PIRATE clusters genes (or other annotated features) over a wide range of amino acid or nucleotide identity thresholds and uses the clustering information to rapidly identify paralogous gene families and putative fission/fusion events. Furthermore, PIRATE orders the pangenome using a directed graph, provides a measure of allelic variation, and estimates sequence divergence for each gene family. Conclusions We demonstrate that PIRATE scales linearly with both number of samples and computation resources, allowing for analysis of large genomic datasets, and compares favorably to other popular tools. PIRATE provides a robust framework for analysing bacterial pangenomes, from largely clonal to panmictic species.
Author Listing: Sion C Bayliss;Harry A Thorpe;Nicola M Coyle;Samuel K Sheppard;Edward J Feil
Volume: 8
Pages: None
DOI: 10.1093/gigascience/giz119
Language: English
Journal: GigaScience

GigaScience

GIGASCIENCE

影响因子:3.9
是否综述期刊:否
是否OA:是
是否预警:不在预警名单内
发行时间:2012
ISSN:2047-217X
发刊频率:-
收录数据库:SCIE/Scopus收录/DOAJ开放期刊
出版国家/地区:ENGLAND
出版社:BioMed Central

期刊介绍

GigaScience aims to revolutionize data dissemination, organization, understanding, and use. An online open-access open-data journal, we publish 'big-data' studies from the entire spectrum of life and biomedical sciences. To achieve our goals, the journal has a novel publication format: one that links standard manuscript publication with an extensive database ([GigaDB](http://gigadb.org/)) that hosts all associated data, as well as provides data analysis tools through our [GigaGalaxy](http://galaxy.cbiit.cuhk.edu.hk/) server. Further promoting transparency in the review process, we have open review as standard for all our peer-reviewed papers.Our scope covers not just 'omic' type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale shareable data.

GigaScience旨在彻底改变数据传播、组织、理解和使用。作为一个在线开放获取的开放数据期刊,我们发表来自生命和生物医学科学整个领域的“大数据”研究。为实现我们的目标,该刊有一种新颖的出版格式:一个将标准手稿出版物与一个广泛的数据库([GigaDB](http://gigadb.org/))连接起来的平台,该数据库托管所有相关数据,并通过我们的[GigaGalaxy](http://galaxy.cbiit.cuhk.edu.hk/)服务器提供数据分析工具。为了进一步提高评审过程的透明度,我们将开放式评审作为所有同行评审论文的标准。我们的范围不仅涵盖“组学”类型的数据和目前由大型公共知识库提供服务的高通量生物学领域,还涵盖越来越多的更难获取的数据,如成像、神经科学、生态学、队列数据、系统生物学和其他新型的大规模可共享数据。

年发文量 111
国人发稿量 23
国人发文占比 20.59%
自引率 2.6%
平均录取率 -
平均审稿周期 1 Weeks
版面费 US$2415
偏重研究方向 MULTIDISCIPLINARY SCIENCES-
期刊官网 https://academic.oup.com/gigascience
投稿链接 https://www.editorialmanager.com/GIGA

质量指标占比

研究类文章占比 OA被引用占比 撤稿占比 出版后修正文章占比
97.30% 97.61% 0.00% 3.88%

相关指数

影响因子
影响因子
年发文量
自引率
Cite Score

预警情况

时间 预警情况
2025年03月发布的2025版 不在预警名单中
2024年02月发布的2024版 不在预警名单中
2023年01月发布的2023版 不在预警名单中
2021年12月发布的2021版 不在预警名单中
2020年12月发布的2020版 不在预警名单中

JCR分区 WOS分区等级:Q1区

版本 按学科 分区
WOS期刊SCI分区
(2021-2022年最新版)
MULTIDISCIPLINARY SCIENCES Q1

中科院分区

版本 大类学科 小类学科 Top期刊 综述期刊
生物学
2区
BIOLOGY
生物学
2区
2021年12月
基础版
生物
2区
MULTIDISCIPLINARY SCIENCES
综合性期刊
2区
2021年12月
升级版
生物学
2区
MULTIDISCIPLINARY SCIENCES
综合性期刊
2区
2020年12月
旧的升级版
生物学
2区
MULTIDISCIPLINARY SCIENCES
综合性期刊
2区
2022年12月
最新升级版
生物学
2区
MULTIDISCIPLINARY SCIENCES
综合性期刊
2区