NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy.
NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy.
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DOI：
10.1093/gigascience/giaa105
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发表时间：
2020-10-17
期刊：
影响因子：
9.2
通讯作者：
Stubbs AP
中科院分区：
文献类型：
--
作者：
de Koning W;Miladi M;Hiltemann S;Heikema A;Hays JP;Flemming S;van den Beek M;Mustafa DA;Backofen R;Grüning B;Stubbs AP
长读长测序可用于以相对较低的成本和最少的样品制备生成非常长的重叠群，甚至完全组装的基因组。因此，长读长测序平台变得越来越流行。在这方面，基于牛津纳米孔技术公司的长读长测序“纳米孔”平台正在成为一种广泛使用的工具，具有广泛的应用和最终用户。然而，探索和操作长读长测序平台生成的复杂数据的需要需要附带专门的生物信息学平台和工具来正确处理长读长数据。重要的是，此类工具还应通过为研究人员提供轻松访问和易用的解决方案来帮助实现生物信息学分析的民主化。 Galaxy 平台为基于命令行的计算工具提供了用户友好的界面，处理软件依赖性，并提供完善的工作流程。用户不必具备编程经验或扩展的计算机技能。该界面使研究人员能够执行强大的生物信息学分析，包括短读或长读序列数据的组装和分析。新开发的“NanoGalaxy”是一款基于Galaxy的工具包，用于分析长读长测序数据，适用于多种应用，包括从基因组、宏基因组和质粒序列读长进行从头基因组组装。一系列用于长读序列基因组组装的最佳实践工具和工作流程已集成到 NanoGalaxy 平台中，以方便研究人员轻松访问和使用生物信息学工具。 NanoGalaxy 可在欧洲 Galaxy 服务器 https://nanopore.usegalaxy.eu 上免费获取，并可在 https://training.galaxyproject.org 上获取支持的自学培训材料。
Long-read sequencing can be applied to generate very long contigs and even completely assembled genomes at relatively low cost and with minimal sample preparation. As a result, long-read sequencing platforms are becoming more popular. In this respect, the Oxford Nanopore Technologies–based long-read sequencing “nanopore" platform is becoming a widely used tool with a broad range of applications and end-users. However, the need to explore and manipulate the complex data generated by long-read sequencing platforms necessitates accompanying specialized bioinformatics platforms and tools to process the long-read data correctly. Importantly, such tools should additionally help democratize bioinformatics analysis by enabling easy access and ease-of-use solutions for researchers. The Galaxy platform provides a user-friendly interface to computational command line–based tools, handles the software dependencies, and provides refined workflows. The users do not have to possess programming experience or extended computer skills. The interface enables researchers to perform powerful bioinformatics analysis, including the assembly and analysis of short- or long-read sequence data. The newly developed “NanoGalaxy" is a Galaxy-based toolkit for analysing long-read sequencing data, which is suitable for diverse applications, including de novo genome assembly from genomic, metagenomic, and plasmid sequence reads. A range of best-practice tools and workflows for long-read sequence genome assembly has been integrated into a NanoGalaxy platform to facilitate easy access and use of bioinformatics tools for researchers. NanoGalaxy is freely available at the European Galaxy server https://nanopore.usegalaxy.eu with supporting self-learning training material available at https://training.galaxyproject.org.
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影响因子：
4.5
作者：
de Koning AP;Gu W;Castoe TA;Batzer MA;Pollock DD
通讯作者：
Pollock DD
影响因子：
48
作者：
Flusberg, Benjamin A.;Webster, Dale R.;Lee, Jessica H.;Travers, Kevin J.;Olivares, Eric C.;Clark, Tyson A.;Korlach, Jonas;Turner, Stephen W.
通讯作者：
Turner, Stephen W.
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作者：
Mitsuhashi S;Kryukov K;Nakagawa S;Takeuchi JS;Shiraishi Y;Asano K;Imanishi T
通讯作者：
Imanishi T
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
影响因子：
14.9
作者：
Krawczyk PS;Lipinski L;Dziembowski A
通讯作者：
Dziembowski A