GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.
GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.
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GAAP：原核基因组的基因组组织框架辅助组装管道。
DOI：
10.1186/s12864-016-3267-0
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发表时间：
2017-01-25
期刊：
影响因子：
4.4
通讯作者：
Kang Y
中科院分区：
文献类型：
--
作者：
Yuan L;Yu Y;Zhu Y;Li Y;Li C;Li R;Ma Q;Siu GK;Yu J;Jiang T;Xiao J;Kang Y
背景下一代测序技术极大地促进了原核生物的基因组研究。然而，由于来自NGS的短读段而导致的高度片段化的组装仍然是深入了解基因组生物学的限制因素。参考辅助工具是有前途的基因组组装，但往往会导致错误的装配时，分配的参考有广泛rearrangements. ResultsHereby，我们提出的GAAP，基因组组装管道支架的基础上核心基因定义的基因组组织框架（cGOF）在我们以前的研究中所描述的。我们使用多个参考衍生的cGOF作为索引来帮助支架的顺序和方向并构建骨架结构，而不是分配参考，然后使用读取对来延伸支架，称为局部支架，并区分支架中的真实和嵌合邻接。在我们的性能测试中，使用具有不同基因组大小，复杂性和所有三类cGOF的六个物种的15个基因组的经验和模拟数据，GAAP与其他三个参考辅助程序AlignGraph，Ragout和MeDuSa相比，竞争或获得相当的结果。并且比当前可用的参考辅助组装工具表现得更好，因为它恢复了更多的组装并且产生了更少的错误位置，特别是对于具有广泛重排基因组的物种。我们的方法是一个很有前途的解决方案，从NGS的短读段重建基因组序列。
BackgroundNext-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology. Reference-assisted tools are promising in genome assembly, but tend to result in false assembly when the assigned reference has extensive rearrangements.ResultsHerein, we present GAAP, a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Framework (cGOF) described in our previous study. Instead of assigning references, we use the multiple-reference-derived cGOFs as indexes to assist in order and orientation of the scaffolds and build a skeleton structure, and then use read pairs to extend scaffolds, called local scaffolding, and distinguish between true and chimeric adjacencies in the scaffolds. In our performance tests using both empirical and simulated data of 15 genomes in six species with diverse genome size, complexity, and all three categories of cGOFs, GAAP outcompetes or achieves comparable results when compared to three other reference-assisted programs, AlignGraph, Ragout and MeDuSa.ConclusionsGAAP uses both cGOF and pair-end reads to create assemblies in genomic scale, and performs better than the currently available reference-assisted assembly tools as it recovers more assemblies and makes fewer false locations, especially for species with extensive rearranged genomes. Our method is a promising solution for reconstruction of genome sequence from short reads of NGS.