The de-novo genome assembly is a challenging computational problem for which several pipelines have been developed. The advent of long-read sequencing technology has resulted in a new set of algorithmic approaches for the assembly process. In this work, we identify that one of these new and fast long-read assembly techniques (using Minimap2 and Miniasm) can be modified for the short-read assembly process. This possibility motivated us to customize a long-read assembly approach for applications in a short-read assembly scenario. Here, we compare and contrast our proposed de-novo assembly pipeline (MiniSR) with three other recently developed programs for the assembly of bacterial and small eukaryotic genomes. We have documented two trade-offs: one between speed and accuracy and the other between contiguity and base-calling errors. Our proposed assembly pipeline shows a good balance in these trade-offs. The resulting pipeline is 6 and 2.2 times faster than the short-read assemblers Spades and SGA, respectively. MiniSR generates assemblies of superior N50 and NGA50 to SGA, although assemblies are less complete and accurate than those from Spades. A third tool, SOAPdenovo2, is as fast as our proposed pipeline but had poorer assembly quality.

中文翻译：

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使用重叠布局共识方法的快速短读De-Novo汇编。

新基因组组装是一个具有挑战性的计算问题，为此已经开发了数条管道。长读测序技术的出现为组装过程带来了一套新的算法​​方法。在这项工作中，我们确定可以针对短读组装过程修改这些新的快速长读组装技术（使用Minimap2和Miniasm）之一。这种可能性促使我们为短读组装方案中的应用程序定制长读组装方法。在这里，我们将拟议的新型装配流水线（MiniSR）与其他三个最近开发的用于细菌和小型真核基因组装配的程序进行比较和对比。我们已经记录了两个权衡：一个在速度和准确性之间，另一个在连续性和碱基检出错误之间。我们建议的装配流水线显示了这些折衷之间的良好平衡。生成的流水线分别比短读汇编程序Spades和SGA快6倍和2.2倍。尽管MiniSR的装配不如Spades完整和准确，但MiniSR产生的N50和NGA50优于SGA。第三种工具SOAPdenovo2与我们建议的管道速度一样快，但装配质量较差。