De novo assembly of bacterial genomes with repetitive DNA regions by dnaasm application.
De novo assembly of bacterial genomes with repetitive DNA regions by dnaasm application.
复制标题
通过施用DNAASM的重复DNA区域的细菌基因组的从头组装。
DOI：
10.1186/s12859-018-2281-4
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发表时间：
2018-07-18
影响因子：
3
通讯作者：
Nowak R
中科院分区：
文献类型：
--
作者：
Kuśmirek W;Nowak R
许多生物体，特别是细菌，含有称为串联重复序列的重复DNA片段。这些结构是由DNA组装者通过将成对的末端标签映射到单元，估计它们之间的距离，并用指定的DNA基序填充间隙来修复的，这可以重复多次。然而，一些串联重复序列比成对末端标签之间的距离长。我们提出了一种新的从头DNA组装算法，该算法使用读取的相对频率来适当地恢复串联重复序列。该算法的主要优点是可以很好地恢复远长于最大读取长度的串联重复序列和成对末端标签的插入长度。此外，仅被单读测序数据覆盖的重复DNA区域也可以被恢复。在这种情况下，其他现有的从头组装DNA的程序也会失败。提出的应用程序由几个步骤组成，包括：(i)构建de Bruijn图，（ii）纠正de Bruijn图，（iii）归一化边缘权重，以及（iv）生成DNA序列的输出集。我们在细菌有机体的真实数据集上测试了我们的方法。开发了软件库、控制台应用程序和web应用程序。Web应用程序采用客户端-服务器架构开发，其中Web浏览器用于与最终用户通信，算法使用c++和Python实现。所提出的方法能够正确地重建串联重复序列，这比成对末端标签的插入尺寸要长。该应用程序在GNU库或LGPLv3（较宽松通用公共许可证版本3.0）下免费提供给所有用户。
Many organisms, in particular bacteria, contain repetitive DNA fragments called tandem repeats. These structures are restored by DNA assemblers by mapping paired-end tags to unitigs, estimating the distance between them and filling the gap with the specified DNA motif, which could be repeated many times. However, some of the tandem repeats are longer than the distance between the paired-end tags. We present a new algorithm for de novo DNA assembly, which uses the relative frequency of reads to properly restore tandem repeats. The main advantage of the presented algorithm is that long tandem repeats, which are much longer than maximum reads length and the insert size of paired-end tags can be properly restored. Moreover, repetitive DNA regions covered only by single-read sequencing data could also be restored. Other existing de novo DNA assemblers fail in such cases. The presented application is composed of several steps, including: (i) building the de Bruijn graph, (ii) correcting the de Bruijn graph, (iii) normalizing edge weights, and (iv) generating the output set of DNA sequences. We tested our approach on real data sets of bacterial organisms. The software library, console application and web application were developed. Web application was developed in client-server architecture, where web-browser is used to communicate with end-user and algorithms are implemented in C++ and Python. The presented approach enables proper reconstruction of tandem repeats, which are longer than the insert size of paired-end tags. The application is freely available to all users under GNU Library or Lesser General Public License version 3.0 (LGPLv3).
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