An integrated SNP mining and utilization (ISMU) pipeline for next generation sequencing data.

Area of Science:

• Bioinformatics
• Genomics
• Plant Breeding

Background:

• Single nucleotide polymorphism (SNP) discovery from next-generation sequencing (NGS) data typically demands advanced computational skills and resources, posing a significant barrier for many biologists.
• Existing SNP data often requires further processing for effective use in downstream applications like genotyping.

Purpose of the Study:

• To develop a comprehensive, user-friendly pipeline for both SNP discovery and the subsequent development of genotyping assays.
• To integrate various open-source NGS tools into a single, accessible platform, thereby streamlining the SNP analysis workflow.

Main Methods:

• The Integrated SNP Mining and Utilization (ISMU) pipeline was developed, incorporating functionalities for raw data pre-processing, alignment (Bowtie2, BWA, Maq, NovoAlign, SOAP2), and SNP prediction (SAMtools/SOAPsnp/CNS2snp, CbCC).
• It includes interfaces for developing genotyping assays (KASP, Golden Gate) and integrates visualization tools (Tablet, Flapjack) for alignment inspection.
• The pipeline processes diverse NGS data types (whole genome, RAD-seq, transcriptome) and provides confidence scores for identified SNPs.

Main Results:

• The ISMU pipeline successfully identifies high-quality SNPs across pairwise genotype combinations.
• It generates SNP data in a standardized format suitable for direct use in marker genotyping assay development.
• Visualization tools aid in the inspection of sequence alignments and potential errors.

Conclusions:

• The ISMU pipeline democratizes SNP discovery and utilization for researchers, particularly in plant genetics and breeding, by removing computational barriers.
• It offers a fast, efficient, and parallelized solution for processing large NGS datasets, accelerating genomic studies.
• The software is freely available as a standalone Java application.