Exploiting the great potential of Sequence Capture data by a new tool, SUPER-CAP. (8th December 2016)

• Record Type: Journal Article
• Authors: Ruggieri, Valentino; Anzar, Irantzu; Paytuvi, Andreu; Calafiore, Roberta; Cigliano, Riccardo Aiese; Sanseverino, Walter; Barone, Amalia
• Is Part Of: DNA research. Volume 24:Number 1(2017:Feb.)
• Page Start: 81
• Page End: 91
• Publication Date: 2016-12-08
• Subjects: target enrichment -- sequence reconstruction -- heterozygous variants -- web tool analysis; Genes -- Periodicals; Genomes -- Periodicals; Genes -- Research -- Periodicals; Genomics -- Periodicals; DNA -- Research -- Periodicals; 572.86072
• DOI: 10.1093/dnares/dsw050
• Languages: English
• ISSNs: 1340-2838

Abstract

Abstract: The recent development of Sequence Capture methodology represents a powerful strategy for enhancing data generation to assess genetic variation of targeted genomic regions. Here, we present SUPER-CAP, a bioinformatics web tool aimed at handling Sequence Capture data, fine calculating the allele frequency of variations and building genotype-specific sequence of captured genes. The dataset used to develop this in silico strategy consists of 378 loci and related regulative regions in a collection of 44 tomato landraces. About 14, 000 high-quality variants were identified. The high depth (>40×) of coverage and adopting the correct filtering criteria allowed identification of about 4, 000 rare variants and 10 genes with a different copy number variation. We also show that the tool is capable to reconstruct genotype-specific sequences for each genotype by using the detected variants. This allows evaluating the combined effect of multiple variants in the same protein. The architecture and functionality of SUPER-CAP makes the software appropriate for a broad set of analyses including SNP discovery and mining. Its functionality, together with the capability to process large data sets and efficient detection of sequence variation, makes SUPER-CAP a valuable bioinformatics tool for genomics and breeding purposes.