Department of Mathematical, Physical and Computer Sciences, University of Parma, 43124 Parma, Italy.
Department of Computer Science, University of Verona, 37134 Verona, Italy.
Bioinformatics. 2022 Apr 28;38(9):2631-2632. doi: 10.1093/bioinformatics/btac158.
Computational tools for pangenomic analysis have gained increasing interest over the past two decades in various applications such as evolutionary studies and vaccine development. Synthetic benchmarks are essential for the systematic evaluation of their performance. Currently, benchmarking tools represent a genome as a set of genetic sequences and fail to simulate the complete information of the genomes, which is essential for evaluating pangenomic detection between fragmented genomes.
We present PANPROVA, a benchmark tool to simulate prokaryotic pangenomic evolution by evolving the complete genomic sequence of an ancestral isolate. In this way, the possibility of operating in the preassembly phase is enabled. Gene set variations, sequence variation and horizontal acquisition from a pool of external genomes are the evolutionary features of the tool.
PANPROVA is publicly available at https://github.com/InfOmics/PANPROVA. The manuscript explicitelly refers to the github repository.
Supplementary data are available at Bioinformatics online.
在过去的二十年中，计算工具在各种应用中，如进化研究和疫苗开发中，对泛基因组分析的兴趣日益增加。合成基准对于系统评估它们的性能至关重要。目前，基准工具将基因组表示为一组遗传序列，无法模拟基因组的完整信息，而这对于评估碎片化基因组之间的泛基因组检测至关重要。
我们提出了 PANPROVA，这是一种通过进化祖先分离株的完整基因组序列来模拟原核泛基因组进化的基准工具。这样，就可以在预组装阶段进行操作。基因集变化、序列变化和来自外部基因组池的水平获取是该工具的进化特征。
PANPROVA 可在 https://github.com/InfOmics/PANPROVA 上公开获取。本文明确提到了 github 存储库。
补充数据可在生物信息学在线获得。
