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snpTree - a web-server to identify and construct SNP trees from whole genome sequence data

机译：snpTree-用于从全基因组序列数据中识别和构建SNP树的Web服务器

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Background The advances and decreasing economical cost of whole genome sequencing (WGS), will soon make this technology available for routine infectious disease epidemiology. In epidemiological studies, outbreak isolates have very little diversity and require extensive genomic analysis to differentiate and classify isolates. One of the successfully and broadly used methods is analysis of single nucletide polymorphisms (SNPs). Currently, there are different tools and methods to identify SNPs including various options and cut-off values. Furthermore, all current methods require bioinformatic skills. Thus, we lack a standard and simple automatic tool to determine SNPs and construct phylogenetic tree from WGS data. Results Here we introduce snpTree, a server for online-automatic SNPs analysis. This tool is composed of different SNPs analysis suites, perl and python scripts. snpTree can identify SNPs and construct phylogenetic trees from WGS as well as from assembled genomes or contigs. WGS data in fastq format are aligned to reference genomes by BWA while contigs in fasta format are processed by Nucmer. SNPs are concatenated based on position on reference genome and a tree is constructed from concatenated SNPs using FastTree and a perl script. The online server was implemented by HTML, Java and python script. The server was evaluated using four published bacterial WGS data sets ( V. cholerae , S. aureus CC398, S . Typhimurium and M. tuberculosis ). The evalution results for the first three cases was consistent and concordant for both raw reads and assembled genomes. In the latter case the original publication involved extensive filtering of SNPs, which could not be repeated using snpTree. Conclusions The snpTree server is an easy to use option for rapid standardised and automatic SNP analysis in epidemiological studies also for users with limited bioinformatic experience. The web server is freely accessible at http://www.cbs.dtu.dk/services/snpTree-1.0/ .
机译：背景技术全基因组测序（WGS）的进步和降低的经济成本将很快使该技术可用于常规传染病流行病学。在流行病学研究中，爆发分离株几乎没有多样性，需要进行广泛的基因组分析才能对分离株进行区分和分类。一种成功且广泛使用的方法是对单个核苷酸多态性（SNP）的分析。当前，有多种识别SNP的工具和方法，包括各种选项和临界值。此外，所有当前方法都需要生物信息学技能。因此，我们缺乏一个标准且简单的自动工具来确定SNP并根据WGS数据构建系统树。结果在这里，我们介绍snpTree，这是一种用于在线自动SNP分析的服务器。该工具由不同的SNP分析套件，perl和python脚本组成。 snpTree可以识别SNP，并从WGS以及组装的基因组或重叠群构建系统树。 BWA将fastq格式的WGS数据与参考基因组对齐，而Nucmer处理fasta格式的重叠群。根据参考基因组上的位置将SNP连接起来，并使用FastTree和perl脚本从连接的SNP构建树。在线服务器由HTML，Java和python脚本实现。使用四个已发布的细菌WGS数据集（霍乱弧菌，金黄色葡萄球菌CC398，鼠伤寒沙门氏菌和结核分枝杆菌）对服务器进行了评估。前三个案例的评估结果对于原始读数和组装的基因组都是一致且一致的。在后一种情况下，原始出版物涉及对SNP的广泛过滤，使用snpTree无法重复过滤。结论snpTree服务器是流行病学研究中快速标准化和自动SNP分析的易于使用的选件，也适用于生物信息学经验有限的用户。可从http://www.cbs.dtu.dk/services/snpTree-1.0/免费访问Web服务器。

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