Minimus: a fast, lightweight genome assembler.
Minimus: a fast, lightweight genome assembler.
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DOI：
10.1186/1471-2105-8-64
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发表时间：
2007-02-26
影响因子：
3
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为了应对大型全基因组测序项目的挑战，对算法的需求使得基因组组装器变得非常庞大和复杂。然而，汇编程序的许多最常见用途最好由一种更简单的汇编程序提供，这种汇编程序需要更少的软件组件，使用更少的内存，并且更容易安装和运行。我们开发了Minimus汇编器来解决这些问题，并在一系列汇编问题上进行了测试。我们发现Minimus在几个小型组装任务上表现良好，包括病毒基因组、单个基因和BAC克隆的组装。此外，我们评估了Minimus在组装细菌基因组方面的性能，以评估其作为更大组装管道组成部分的适用性。我们表明，与目前用于这些任务的其他软件不同，Minimus产生的组装错误显著减少，其代价是生成更碎片化的组装。我们发现，对于小基因组和其他小型组装任务，Minimus比现有工具更快、更灵活。由于其小尺寸和模块化设计，Minimus非常适合作为复杂组装管道的组成部分。Minimus作为一个开源软件项目发布，其代码可以在Sourceforge上作为AMOS项目的一部分获得。
Genome assemblers have grown very large and complex in response to the need for algorithms to handle the challenges of large whole-genome sequencing projects. Many of the most common uses of assemblers, however, are best served by a simpler type of assembler that requires fewer software components, uses less memory, and is far easier to install and run. We have developed the Minimus assembler to address these issues, and tested it on a range of assembly problems. We show that Minimus performs well on several small assembly tasks, including the assembly of viral genomes, individual genes, and BAC clones. In addition, we evaluate Minimus' performance in assembling bacterial genomes in order to assess its suitability as a component of a larger assembly pipeline. We show that, unlike other software currently used for these tasks, Minimus produces significantly fewer assembly errors, at the cost of generating a more fragmented assembly. We find that for small genomes and other small assembly tasks, Minimus is faster and far more flexible than existing tools. Due to its small size and modular design Minimus is perfectly suited to be a component of complex assembly pipelines. Minimus is released as an open-source software project and the code is available as part of the AMOS project at Sourceforge.