ToMMo Supercomputer assists to produce data and software tools. iJGVD is a database of genomic variation which released by Tohoku Medical Megabank Organization. HLA-VBseq and TIGAR are software tools which developed at Group of in silico Analysis.
Integrative Japanese Genome Variation Database (iJGVD; http://ijgvd.megabank.tohoku.ac.jp/) provides data of genomic variations obtained by whole-genome sequencing of Japanese individuals who participate the genome cohort study of ToMMo. The current release provides SNV frequency data obtained from the 1070 individuals. The first release contains data of about 4,300,000 SNVs selected by the criteria: (1) they are on autosomes, (2) they exist at least 5.0 % frequency in the 1070 individuals, and (3) they have been reported in dbSNP138.
Japanese Multi Omics Reference Panel, jMorp, is a database of metabolome and proteome data in plasma obtained from volunteers in ToMMo. Metabolome data were measured by proton NMR and LC-MS, and proteome data were obtained by nanoLC-MS. We could measure several thousands of metabolites including the uncharacterized ones, and several hundreds of proteins until now. The data will be released after careful check of each metabolite and protein in order.
TIGAR is a software to estimate gene expression levels of transcript isoforms from RNA-Seq data. Because Bowtie2 or BWA-MEM is utilized for read alignment, the pipeline is better at handling sequencing errors and can achieve robust estimation.
TIGAR (Bioinformatics 2013, Nariai et al. ) TIGAR2 (BMC Genomics 2014, Nariai et al.)