Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, 3851 Fallowfield Road, Nepean, Ontario K2J 4S1, Canada.
Bioinformatics. 2024 Feb 1;40(2). doi: 10.1093/bioinformatics/btae066.
Genomic variations comprise a spectrum of alterations, ranging from single nucleotide polymorphisms (SNPs) to large-scale structural variants (SVs), which play crucial roles in bacterial evolution and species diversification. Accurately identifying SNPs and SVs is beneficial for subsequent evolutionary and epidemiological studies. This study presents VariantDetective (VD), a novel, user-friendly, and all-in-one pipeline combining SNP and SV calling to generate consensus genomic variants using multiple tools.
The VD pipeline accepts various file types as input to initiate SNP and/or SV calling, and benchmarking results demonstrate VD's robustness and high accuracy across multiple tested datasets when compared to existing variant calling approaches.
The source code, test data, and relevant information for VD are freely accessible at https://github.com/OLF-Bioinformatics/VariantDetective under the MIT License.
基因组变异包括一系列的改变，从单核苷酸多态性 (SNPs) 到大规模结构变异 (SVs)，它们在细菌进化和物种多样化中起着至关重要的作用。准确识别 SNPs 和 SVs 有利于后续的进化和流行病学研究。本研究提出了 VariantDetective (VD)，这是一个新颖的、用户友好的、集 SNP 和 SV 调用于一体的综合管道，使用多种工具生成共识基因组变异。
VD 管道接受各种文件类型作为输入，以启动 SNP 和/或 SV 调用，并且基准测试结果表明，与现有的变体调用方法相比，VD 在多个测试数据集上具有稳健性和高精度。
VD 的源代码、测试数据和相关信息可在 MIT 许可证下在 https://github.com/OLF-Bioinformatics/VariantDetective 上免费获取。
