Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection.

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ID: 86685
2019
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Abstract
The development of next generation sequencer (NGS) and the analytical methods allowed the researchers to profile their samples more precisely and easier than before. Especially for agriculture, the certification of the genomic background of their plant materials would be important for the reliability of seed market and stable yield as well as for quarantine procedure. However, the analysis of NGS data is still difficult for non-computational researchers or breeders to verify their samples because majority of current softwares for NGS analysis require users to access unfamiliar Linux environment.Here, we developed a web-application, "Soybean-VCF2Genomes", http://pgl.gnu.ac.kr/soy_vcf2genome/ to map single sample variant call format (VCF) file against known soybean germplasm collection for identification of the closest soybean accession. Based on principal component analysis (PCA), we simplified genotype matrix for lowering computational burden while maintaining accurate clustering. With our web-application, users can simply upload single sample VCF file created by more than 10x resequencing strategy to find the closest samples along with linkage dendrogram of the reference genotype matrix.The information of the closest soybean cultivar will allow breeders to estimate relative germplasmic position of their query sample to determine soybean breeding strategies. Moreover, our VCF2Genomes scheme can be extended to other plant species where the whole genome sequences of core collection are publicly available.
Reference Key
ha2019soybeanvcf2genomesbmc Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Ha, Jungmin;Jeon, Ho Hwi;Woo, Dong U;Lee, Yejin;Park, Halim;Lee, Joohyeong;Kang, Yang Jae;
Journal BMC Bioinformatics
Year 2019
DOI
10.1186/s12859-019-2859-5
URL
Keywords
Machine learning next generation sequencing soybean genome-based breeding germplasm identification

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