Azam, S and Rathore, A and Shah, T and Mohan, T and Amindala, BP and Ruperao, P and Katta, M A V S K and Varshney, R K (2014) An Integrated SNP Mining and Utilization (ISMU) Pipeline for Next Generation Sequencing Data. PLoS ONE, 9 (7). pp. 1-11. ISSN 1932-6203
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Abstract
Open source single nucleotide polymorphism (SNP) discovery pipelines for next generation sequencing data commonly requires working knowledge of command line interface, massive computational resources and expertise which is a daunting task for biologists. Further, the SNP information generated may not be readily used for downstream processes such as genotyping. Hence, a comprehensive pipeline has been developed by integrating several open source next generation sequencing (NGS) tools along with a graphical user interface called Integrated SNP Mining and Utilization (ISMU) for SNP discovery and their utilization by developing genotyping assays. The pipeline features functionalities such as pre-processing of raw data, integration of open source alignment tools (Bowtie2, BWA, Maq, NovoAlign and SOAP2), SNP prediction (SAMtools/SOAPsnp/CNS2snp and CbCC) methods and interfaces for developing genotyping assays. The pipeline outputs a list of high quality SNPs between all pairwise combinations of genotypes analyzed, in addition to the reference genome/sequence. Visualization tools (Tablet and Flapjack) integrated into the pipeline enable inspection of the alignment and errors, if any. The pipeline also provides a confidence score or polymorphism information content value with flanking sequences for identified SNPs in standard format required for developing marker genotyping (KASP and Golden Gate) assays. The pipeline enables users to process a range of NGS datasets such as whole genome re-sequencing, restriction site associated DNA sequencing and transcriptome sequencing data at a fast speed. The pipeline is very useful for plant genetics and breeding community with no computational expertise in order to discover SNPs and utilize in genomics, genetics and breeding studies. The pipeline has been parallelized to process huge datasets of next generation sequencing. It has been developed in Java language and is available at http://hpc.icrisat.cgiar.org/ISMU as a standalone free software.
| Item Type: | Article |
|---|---|
| Divisions: | RP-Dryland Cereals RP-Grain Legumes |
| CRP: | CGIAR Research Program on Dryland Cereals CGIAR Research Program on Grain Legumes |
| Subjects: | Others > Genetics and Genomics |
| Depositing User: | Mr Siva Shankar |
| Date Deposited: | 15 Jul 2014 03:43 |
| Last Modified: | 15 Jul 2014 03:43 |
| URI: | http://oar.icrisat.org/id/eprint/8205 |
| Official URL: | http://dx.doi.org/10.1371/journal.pone.0101754 |
| Projects: | UNSPECIFIED |
| Funders: | CGIAR Generation Challenge Program (GCP), Mexico |
| Acknowledgement: | The authors confirm that all data underlying the findings are fully available without restriction. Genomic data can be accessed from http:// hpc.icrisat.cgiar.org/ISMU/datasets/, while RNASeq dataset are publicly available at SRA with accession numbers SRR647081 and SRR647076 (http://www.ncbi. nlm.nih.gov/sra). |
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