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Kmasker plants - a tool for assessing complex sequence space in plant species.
The Plant Journal ( IF 7.2 ) Pub Date : 2020-01-11 , DOI: 10.1111/tpj.14645
Sebastian Beier 1 , Chris Ulpinnis 2 , Markus Schwalbe 1 , Thomas Münch 1 , Robert Hoffie 1 , Iris Koeppel 1 , Christian Hertig 1 , Nagaveni Budhagatapalli 1 , Stefan Hiekel 1 , Krishna M Pathi 1 , Goetz Hensel 1 , Martin Grosse 1 , Sindy Chamas 1 , Sophia Gerasimova 1 , Jochen Kumlehn 1 , Uwe Scholz 1 , Thomas Schmutzer 3
Affiliation  

Many plant genomes display high levels of repetitive sequences. The assembly of these complex genomes using short high-throughput sequence reads is still a challenging task. Underestimation or disregard of repeat complexity in these datasets can easily misguide downstream analysis. Detection of repetitive regions by k-mer counting methods has proved to be reliable. Easy-to-use applications utilizing k-mer counting are in high demand, especially in the domain of plants. We present Kmasker plants, a tool that uses k-mer count information as an assistant throughout the analytical workflow of genome data that is provided as a command-line and web-based solution. Beside its core competence to screen and mask repetitive sequences, we have integrated features that enable comparative studies between different cultivars or closely related species and methods that estimate target specificity of guide RNAs for application of site-directed mutagenesis using Cas9 endonuclease. In addition, we have set up a web service for Kmasker plants that maintains pre-computed indices for 10 of the economically most important cultivated plants. Source code for Kmasker plants has been made publically available at https://github.com/tschmutzer/kmasker. The web service is accessible at https://kmasker.ipk-gatersleben.de.

中文翻译:

Kmasker植物-一种评估植物物种中复杂序列空间的工具。

许多植物基因组显示出高水平的重复序列。使用短的高通量序列读数组装这些复杂的基因组仍然是一项艰巨的任务。在这些数据集中低估或忽略重复复杂性很容易误导下游分析。通过k-mer计数方法检测重复区域已被证明是可靠的。对使用k-mer计数的易于使用的应用有很高的要求,尤其是在植物领域。我们介绍了Kmasker植物,这是一种在整个基因组数据分析工作流程中使用k-mer计数信息作为辅助工具的工具,该工具作为命令行和基于Web的解决方案提供。除了筛选和掩盖重复序列的核心能力外,我们具有整合的功能,可以在不同品种或密切相关的物种之间进行比较研究,并可以估计使用Cas9核酸内切酶进行定向诱变的指导RNA靶标特异性的方法。此外,我们还为Kmasker植物建立了一个Web服务,该服务为10个经济上最重要的栽培植物保持预先计算的指数。Kmasker工厂的源代码已在https://github.com/tschmutzer/kmasker上公开提供。可通过https://kmasker.ipk-gatersleben.de访问该Web服务。Kmasker工厂的源代码已在https://github.com/tschmutzer/kmasker上公开提供。可通过https://kmasker.ipk-gatersleben.de访问该Web服务。Kmasker工厂的源代码已在https://github.com/tschmutzer/kmasker上公开提供。可通过https://kmasker.ipk-gatersleben.de访问该Web服务。
更新日期:2020-01-11
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