ppsPCP：一种植物存在/缺失变体扫描和泛基因组构建管道。
ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline.
机构信息
National Key Laboratory of Crop Genetic Improvement.
Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China.
出版信息
Bioinformatics. 2019 Oct 15;35(20):4156-4158. doi: 10.1093/bioinformatics/btz168.
SUMMARY
Since the idea of pan-genomics emerged several tools and pipelines have been introduced for prokaryotic pan-genomics. However, not a single comprehensive pipeline has been reported which could overcome multiple challenges associated with eukaryotic pan-genomics. To aid the eukaryotic pan-genomic studies, here we present ppsPCP pipeline which is designed for eukaryotes especially for plants. It is capable of scanning presence/absence variants (PAVs) and constructing a fully annotated pan-genome. We believe with these unique features of PAV scanning and building a pan-genome together with its annotation, ppsPCP will be useful for plant pan-genomic studies and aid researchers to study genetic/phenotypic variations and genomic diversity.
AVAILABILITY AND IMPLEMENTATION
The ppsPCP is freely available at github DOI: https://doi.org/10.5281/zenodo.2567390 and webpage http://cbi.hzau.edu.cn/ppsPCP/.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
自从泛基因组学的概念出现以来，已经有许多工具和流程被引入到原核生物的泛基因组学中。然而，目前还没有一个综合性的流程能够克服真核生物泛基因组学所面临的多种挑战。为了辅助真核生物的泛基因组学研究，我们在这里提出了 ppsPCP 流程，它是专门为真核生物设计的，特别是针对植物。它能够扫描存在/缺失变异（PAVs）并构建一个全注释的泛基因组。我们相信，凭借 PAV 扫描的这些独特功能以及构建一个包含注释的泛基因组，ppsPCP 将有助于植物的泛基因组研究，并帮助研究人员研究遗传/表型变异和基因组多样性。
可用性和实现
ppsPCP 可在 github 的 DOI：https://doi.org/10.5281/zenodo.2567390 以及网页 http://cbi.hzau.edu.cn/ppsPCP/ 上免费获取。
补充信息
补充数据可在生物信息学在线获取。
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