ISMU: Integrated SNP Mining and Utilization Pipeline For Accelerated Breeding

Detection of variants from Next Generation Sequencing (NGS) data is often complicated and requires various methodologies and multiple steps. An effort has been undertaken to include all the steps in a user-friendly pipeline which we defined as Integrated SNP Mining and Utilization (ISMU) pipeline. After pre-processing the raw data, the pipeline provides users a range of options for alignment using tools such as Bowtie, BWA, SOAP, Maq and NovoAlign. The tools which provide alignments in SAM format, are then processed for SNP prediction with SAM tools, otherwise existing packages within the programs such as SOAPsnp and cns2snp (Maq) are used. The Coverage based Consensus Calling (CbCC) approach is integrated with all alignment tools (Azam et al, 2012, AM J BOT, 99:186–192). The output after analyzing NGS data through this pipeline includes list of SNPs between any combination of genotypes. Tablet and Flapjack have also been integrated into the pipeline to allow users to visualise the alignment and SNPs respectively. For further validation on array based SNP platforms, users can 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 been developed to run on 64-bit Linux. The server edition is written in CGI Perl while standalone version is developed in Java. In the next phase of ISMU efforts are underway to integrate genomic selection (GS) and marker assisted recurrent selection (MARS) modules to utilize SNPs data for accelerated breeding programs.