Journal article
An Integrated SNP Mining and Utilization (ISMU) pipeline for next generation sequencing data
PLoS ONE, Vol.9(7), Art. e101754
2014
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.
Details
- Title
- An Integrated SNP Mining and Utilization (ISMU) pipeline for next generation sequencing data
- Authors/Creators
- M. Prasad (Author/Creator)S. Azam (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsA. Rathore (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsT.M. Shah (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsM. Telluri (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsB.P. Amindala (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsP. Ruperao (Author/Creator) - The University of QueenslandM.A.V.S.K. Katta (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsR.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
- Publication Details
- PLoS ONE, Vol.9(7), Art. e101754
- Publisher
- Public Library of Science
- Identifiers
- 991005543064807891
- Copyright
- © 2021 The Authors.
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
UN Sustainable Development Goals (SDGs)
This output has contributed to the advancement of the following goals:
Source: InCites
Metrics
9 File views/ downloads
62 Record Views
InCites Highlights
These are selected metrics from InCites Benchmarking & Analytics tool, related to this output
- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Biotechnology & Applied Microbiology
- ESI research areas
- Molecular Biology & Genetics