Hierarchical scaffolding with Bambus.
Hierarchical scaffolding with Bambus.
复制标题
DOI：
10.1101/gr.1536204
复制
发表时间：
2003-12
期刊：
影响因子：
7
通讯作者：
Mihai Pop;D. Kosack;S. Salzberg
中科院分区：
文献类型：
--
作者：
Mihai Pop;D. Kosack;S. Salzberg
基因组组装器的输出通常包括连续DNA序列（重叠群）的集合，其沿基因组的相对位置沿着未被定义。通常使用称为支架的程序来使用成对的读取信息对这些重叠群进行排序和定向。这种重叠群的排序是完成和分析全基因组鸟枪计划数据的重要步骤。大多数最近的汇编器包括一个脚手架模块;然而，用户几乎无法控制脚手架算法或生成的信息。因此，我们开发了一个通用的脚手架，称为Bambus，它为用户提供了显着的灵活性，在控制脚手架参数。Bambus最近被用于构建低覆盖率的狗基因组数据草案。最重要的是，Bambus允许使用链接数据，而不是从配对信息中推断出来的数据。例如，完整基因组的序列可以用于指导相关生物体的支架。我们提出了几个应用Bambus：支持整理，比较基因组学，分析基因组的单倍型结构，并在低覆盖率的哺乳动物基因组的脚手架。Bambus是一个开源软件包，可以从我们的网站上获得。
The output of a genome assembler generally comprises a collection of contiguous DNA sequences (contigs) whose relative placement along the genome is not defined. A procedure called scaffolding is commonly used to order and orient these contigs using paired read information. This ordering of contigs is an essential step when finishing and analyzing the data from a whole-genome shotgun project. Most recent assemblers include a scaffolding module; however, users have little control over the scaffolding algorithm or the information produced. We thus developed a general-purpose scaffolder, called Bambus, which affords users significant flexibility in controlling the scaffolding parameters. Bambus was used recently to scaffold the low-coverage draft dog genome data. Most significantly, Bambus enables the use of linking data other than that inferred from mate-pair information. For example, the sequence of a completed genome can be used to guide the scaffolding of a related organism. We present several applications of Bambus: support for finishing, comparative genomics, analysis of the haplotype structure of genomes, and scaffolding of a mammalian genome at low coverage. Bambus is available as an open-source package from our Web site.