Scaffolding pre-assembled contigs using SSPACE
Scaffolding pre-assembled contigs using SSPACE
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DOI：
10.1093/bioinformatics/btq683
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发表时间：
2011-02-15
期刊：
影响因子：
5.8
通讯作者：
Pirovano, Walter
中科院分区：
文献类型：
--
作者：
Boetzer, Marten;Henkel, Christiaan V.;Pirovano, Walter
从头组装工具在从下一代测序（NGS）数据重建基因组中发挥主要作用，并且通常产生许多重叠群。使用配对读取测序数据，可以评估重叠群的顺序、距离和方向，并将它们联合收割机组合成所谓的支架。虽然后一个过程是完成基因组的关键步骤，但支架算法通常是从头组装工具中的内置功能，无法独立控制。我们在这里提出了一个新的工具，称为SSPACE，这是一个独立的支架预组装的重叠群使用配对读取数据。主要特点是：短的运行时间、双端和/或配偶对数据集的多个文库输入以及具有未映射的序列读段的可能的重叠群延伸。SSPACE在原核生物和真核生物基因组测试集上都显示出有希望的结果，其中初始重叠群的量减少了至少75%。
De novo assembly tools play a main role in reconstructing genomes from next-generation sequencing (NGS) data and usually yield a number of contigs. Using paired-read sequencing data it is possible to assess the order, distance and orientation of contigs and combine them into so-called scaffolds. Although the latter process is a crucial step in finishing genomes, scaffolding algorithms are often built-in functions in de novo assembly tools and cannot be independently controlled. We here present a new tool, called SSPACE, which is a stand-alone scaffolder of pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads. SSPACE shows promising results on both prokaryote and eukaryote genomic testsets where the amount of initial contigs was reduced by at least 75%.