Integrated SNP Mining and Utilisation Pipeline (ISMU) is a comprehensive pipeline with a Graphical User Interface for SNP discovery and genotyping, integrating open source tools. ISMU features functionalities such as pre-processing of raw data, integration of open source alignment tools (Bowtie2, BWA, Maq, NovoAlign and SOAP2) and SNP prediction (samtools/SOAPsnp/CNS2snp and CbCC) methods. The pipeline outputs a list of high quality SNPs between all pairwise combinations of genotypes analyzed. Visualization tools (Tablet and Flapjack) have also been integrated into the pipeline to allow inspection of the alignment and SNPs. For further validation on array based SNP platforms, users could select SNPs based on confidence score or PIC values with flanking sequences in a standard format for developing genotyping (KASPar and Golden Gate) assays. The pipeline has also been parallelized to process huge datasets. It is developed in Java as standalone open source software. ISMU is designed for biologists especially plant molecular breeding community with no computational expertise. Researchers could potentially use it to quickly process the NGS data and thereby obtain biological insights.
Download ISMU V2. This is is a zero installation zip file, users only need unzip and follow the user manual.
For queries and additional information on ISMU contact Dr Abhishek Rathore.