Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
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DOI：
10.1371/journal.pcbi.1005595
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发表时间：
2017-06-01
影响因子：
4.3
通讯作者：
Holt, Kathryn E.
中科院分区：
文献类型：
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作者：
Wick, Ryan R.;Judd, Louise M.;Holt, Kathryn E.
Illumina DNA测序平台生成准确但短的读数，其可用于产生准确但片段化的基因组组装。Pacific Biosciences和Oxford Nanopore Technologies的DNA测序平台可以生成长读段，可以产生完整的基因组组装，但测序更昂贵且容易出错。对组合来自这些互补测序技术的数据以产生更准确的“杂交”组装体存在显著的兴趣。然而，很少有工具能够真正利用这两种类型数据的优势，即短读取的准确性和长读取的结构解析能力。在这里，我们介绍了Unicycler，这是一种用于从短读段和长读段的组合中组装细菌基因组的新工具，它可以产生准确，完整和具有成本效益的组装。Unicycler使用从头组装程序SPAdes从短读段构建初始组装图，然后使用来自短读段和长读段的信息简化图。Unicycler使用一种新的半全局对齐器将长读段与组装图对齐。对合成和真实的读段的测试表明，与其他混合组装器相比，Unicycler可以组装更大的重叠群，错误组装更少，即使在长读段深度和准确性较低的情况下也是如此。Unicycler是开源的（GPL v3），可在github.com/rrwick/Unicycler上获得。
The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long reads that can produce complete genome assemblies, but the sequencing is more expensive and errorprone. There is significant interest in combining data from these complementary sequencing technologies to generate more accurate "hybrid" assemblies. However, few tools exist that truly leverage the benefits of both types of data, namely the accuracy of short reads and the structural resolving power of long reads. Here we present Unicycler, a new tool for assembling bacterial genomes from a combination of short and long reads, which produces assemblies that are accurate, complete and cost-effective. Unicycler builds an initial assembly graph from short reads using the de novo assembler SPAdes and then simplifies the graph using information from short and long reads. Unicycler uses a novel semi-global aligner to align long reads to the assembly graph. Tests on both synthetic and real reads show Unicycler can assemble larger contigs with fewer misassemblies than other hybrid assemblers, even when long-read depth and accuracy are low. Unicycler is open source (GPLv3) and available at github.com/rrwick/Unicycler.