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Abstract：
BACKGROUND: Structural variations play an important role in bacterial genomes. They can mediate genome adaptation quickly in response to the external environment and thus can also play a role in antibiotic resistance. The detection of structural variations in bacteria is challenging, and the recognition of even small rearrangements can be important. Even though most detection tools are aimed at and benchmarked on eukaryotic genomes, they can also be used on prokaryotic genomes. The key features of detection are the ability to detect small rearrangements and support haploid genomes. Because of the limiting performance of a single detection tool, combining the detection abilities of multiple tools can lead to more robust results. There are already available workflows for structural variation detection for long-reads technologies and for the detection of single-nucleotide variation and indels, both aimed at bacteria. Yet we are unaware of structural variations detection workflows for the short-reads sequencing platform. Motivated by this gap we created our workflow. Further, we were interested in increasing the detection performance and providing more robust results.
RESULTS: We developed an open-source bioinformatics pipeline, ProcaryaSV, for the detection of structural variations in bacterial isolates from paired-end short sequencing reads. Multiple tools, starting with quality control and trimming of sequencing data, alignment to the reference genome, and multiple structural variation detection tools, are integrated. All the partial results are then processed and merged with an in-house merging algorithm. Compared with a single detection approach, ProcaryaSV has improved detection performance and is a reproducible easy-to-use tool.
CONCLUSIONS: The ProcaryaSV pipeline provides an integrative approach to structural variation detection from paired-end next-generation sequencing of bacterial samples. It can be easily installed and used on Linux machines. It is publicly available on GitHub at https://github.com/robinjugas/ProcaryaSV .
RESULTS: We developed an open-source bioinformatics pipeline, ProcaryaSV, for the detection of structural variations in bacterial isolates from paired-end short sequencing reads. Multiple tools, starting with quality control and trimming of sequencing data, alignment to the reference genome, and multiple structural variation detection tools, are integrated. All the partial results are then processed and merged with an in-house merging algorithm. Compared with a single detection approach, ProcaryaSV has improved detection performance and is a reproducible easy-to-use tool.
CONCLUSIONS: The ProcaryaSV pipeline provides an integrative approach to structural variation detection from paired-end next-generation sequencing of bacterial samples. It can be easily installed and used on Linux machines. It is publicly available on GitHub at https://github.com/robinjugas/ProcaryaSV .
摘要：
背景：结构变异在细菌基因组中起重要作用。它们可以响应于外部环境而快速介导基因组适应，因此也可以在抗生素抗性中发挥作用。细菌结构变异的检测具有挑战性,即使是很小的重新安排也很重要。尽管大多数检测工具都针对真核生物基因组并以其为基准，它们也可以用于原核生物基因组。检测的关键特征是检测小重排和支持单倍体基因组的能力。由于单个检测工具的性能有限，结合多种工具的检测能力可以得到更可靠的结果。对于长读取技术的结构变异检测以及单核苷酸变异和indel的检测，已经有可用的工作流程。都针对细菌。然而，我们不知道短读数测序平台的结构变异检测工作流程。由于这个差距，我们创建了我们的工作流程。Further,我们有兴趣提高检测性能并提供更可靠的结果。
结果：我们开发了一个开源的生物信息学管道，ProcaryaSV,用于检测来自配对末端短测序读数的细菌分离株的结构变异。多种工具,从测序数据的质量控制和修剪开始，与参考基因组对齐，和多种结构变异检测工具，是集成的。然后处理所有部分结果，并使用内部合并算法进行合并。与单一检测方法相比，ProcaryaSV提高了检测性能，是一种可重复的易于使用的工具。
结论：ProcaryaSV管道提供了一种从细菌样本的配对端下一代测序中进行结构变异检测的综合方法。它可以在Linux机器上轻松安装和使用。它可在GitHub上公开获得，网址为https://github.com/robinjugas/ProcaryaSV。
结果：我们开发了一个开源的生物信息学管道，ProcaryaSV,用于检测来自配对末端短测序读数的细菌分离株的结构变异。多种工具,从测序数据的质量控制和修剪开始，与参考基因组对齐，和多种结构变异检测工具，是集成的。然后处理所有部分结果，并使用内部合并算法进行合并。与单一检测方法相比，ProcaryaSV提高了检测性能，是一种可重复的易于使用的工具。
结论：ProcaryaSV管道提供了一种从细菌样本的配对端下一代测序中进行结构变异检测的综合方法。它可以在Linux机器上轻松安装和使用。它可在GitHub上公开获得，网址为https://github.com/robinjugas/ProcaryaSV。
