Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
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DOI：
10.1371/journal.pone.0112963
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Earl AM
中科院分区：
文献类型：
--
作者：
Walker BJ;Abeel T;Shea T;Priest M;Abouelliel A;Sakthikumar S;Cuomo CA;Zeng Q;Wortman J;Young SK;Earl AM
现代测序技术的进步使我们能够在一天内从一台机器中产生足够的数据来分析数百个细菌基因组。对大量基因组进行测序的这种可能性要求使用完全自动化的方法来产生高质量的组装和变体调用。我们介绍了Pilon，这是一个全自动化的一体化工具，用于更正草稿程序集和调用多种大小的序列变体，包括非常大的插入和删除。Pilon适用于许多类型的序列数据，但当提供来自两个Illumina文库的配对末端数据时，Pilon尤其强大，所述两个Illumina文库具有小的例如180bp和大的例如3-5kb的插入。Pilon通过纠正碱基、修复错误组装和填补缺口，显著改善了草稿基因组组装。对于单倍体和二倍体基因组，Pilon都能以更少的错误产生更连续的基因组，从而能够识别更多的生物相关基因。此外，与最先进的工具相比，Pilon以高精度识别小的变异，其独特之处在于它能够准确地识别包括重复在内的大序列变异和解决大插入。Pilon正被用于改进数千个新基因组的组装，并从数千个临床相关的细菌菌株中识别变种。Pilon以开源软件的形式免费提供。
Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes calls for fully automated methods to produce high-quality assemblies and variant calls. We introduce Pilon, a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions. Pilon works with many types of sequence data, but is particularly strong when supplied with paired end data from two Illumina libraries with small e.g., 180 bp and large e.g., 3–5 Kb inserts. Pilon significantly improves draft genome assemblies by correcting bases, fixing mis-assemblies and filling gaps. For both haploid and diploid genomes, Pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. Furthermore, Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions. Pilon is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains. Pilon is freely available as open source software.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
56.3
作者：
Grad, Yonatan H.;Kirkcaldy, Robert D.;Trees, David;Dordel, Janina;Harris, Simon R.;Goldstein, Edward;Weinstock, Hillard;Parkhill, Julian;Hanage, William P.;Bentley, Stephen;Lipsitch, Marc
通讯作者：
Lipsitch, Marc
影响因子：
1.8
作者：
Cubillos-Ruiz, Andres;Morales, Juan;Zambrano, Maria Mercedes
通讯作者：
Zambrano, Maria Mercedes
影响因子：
3.7
作者：
McEvoy CR;Cloete R;Müller B;Schürch AC;van Helden PD;Gagneux S;Warren RM;Gey van Pittius NC
通讯作者：
Gey van Pittius NC
影响因子：
5.8
作者：
Larkin, M. A.;Blackshields, G.;Higgins, D. G.
通讯作者：
Higgins, D. G.