snpTree 1.1 Article Abstract
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 automatic tool to determine SNPs and construct phylogenetic tree from SNPs data.
Results Here we introduce snpTree server as an online-automatic SNPs analysis. This tool is composed of different SNPs calling suits, perl and python scripts. snpTree can identify SNPs and construct phylogenetic tree from WGS as well as from assembled genomes or contigs. WGS data in fastq format are aligned to reference genomes by SAMtools while contigs in fasta format are processed by nucmer. SNPs were concatenated based on position on reference genome and concatenated SNPs were constructed a tree by FastTree and a perl script. The online server was implemented by PHP, Java and python script.
The server had been evaluated using four published bacterial WGS data sets (V. cholerae, S. aureus CC398, S. Typhimurium ST313 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 their 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-1.1/ .