PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria
PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria
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PIRATE：一种快速且可扩展的泛基因组学工具箱，用于对细菌中不同的直向同源物进行聚类
DOI：
10.1101/598391
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Bayliss S
中科院分区：
文献类型：
--
作者：
Bayliss S
对自然界细菌种群中基因的分布进行分类对于理解进化过程和适应的遗传基础是必不可少的。全基因组测序技术的进步导致公共数据库中保存的细菌基因组数量大幅增加。有一个迫切需要的软件解决方案，能够集群，目录和基因，或其他功能，在越来越大的基因组dataset.ResultsHere，我们提出了一个泛基因组学工具箱，PIRATE（泛基因组迭代细化和阈值评估），它确定和分类在细菌泛基因组中的直链基因家族在广泛的序列相似性阈值。PIRATE建立在最近可扩展的软件开发之上，允许快速询问数千个分离株。PIRATE在广泛的氨基酸或核苷酸身份阈值范围内对基因（或其他注释特征）进行聚类，并使用聚类信息快速识别旁系同源基因家族和推定的裂变/融合事件。此外，PIRATE命令的泛基因组使用有向图，提供了一个衡量等位基因变异，并估计每个基因family.ConclusionsWe的序列分歧表明，PIRATE规模与样本数和计算资源的线性，允许分析大型基因组数据集，并比较有利的其他流行的工具。PIRATE为分析细菌泛基因组提供了一个强大的框架，从大部分克隆到泛繁殖物种。
BackgroundCataloguing 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.ResultsHere 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.ConclusionsWe 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.
影响因子：
3.9
作者：
Argimón S;Abudahab K;Goater RJE;Fedosejev A;Bhai J;Glasner C;Feil EJ;Holden MTG;Yeats CA;Grundmann H;Spratt BG;Aanensen DM
通讯作者：
Aanensen DM
Piggy：一种快速、大规模的细菌基因间区域泛基因组分析工具
DOI：
--
发表时间：
2017
期刊：
bioRxiv
影响因子：
--
作者：
Harry A. Thorpe;S. Bayliss;S. Sheppard;E. Feil
通讯作者：
E. Feil