Followings are tools developed in our lab. For details, please see page of each tool.
| JRG |
JRG (Japanese Reference Genome) is provided as a reference genome for Japanese genome analyses. It was constructed by adding insertions detected in Japanese genomes to the international reference genome, GRCh38. |
| Japonica Array |
The Japonica array ”ジャポニカアレイ®” is the first ever SNP array optimized for Japanese population. The aim of development of Japonica array is not only to facilitate the prospective genomic cohort study conducted by Tohoku Medical Megabank Organization (ToMMo) but also to make a contribution to the genomic medicine studies in Japan. |
| iJGVD |
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. |
| HLA-VBseq |
HLA-VBSeq is software to estimate the most likely HLA types from high-throughput sequencing data. |
| STR-realigner |
STR-realigner is a Java program that extracts and realigns sequence reads in input SAM/BAM file around prespecified short tandem repeat regions. Realigned sequence reads are saved as SAM/BAM format and used for variant calling with existing STR callers. |
| TIGAR |
Transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference |
| Pedigree Caller |
Pedigree Caller considers the pedigree information of individuals for accurate variant calling from the aligned sequencing data. |
| CoalescentSTR |
CoalescentSTR is a statistical method that estimate repeat numbers in a microsatellite region for multiple samples from high-throughput sequencing data. Multiple samples can be handled in one statistical model based on coalescent theory, and accurate estimation of repeat numbers are enabled even for microsatellite regions longer than the length of sequence reads. |
| HapMonster |
HapMonster performs variant calling and haplotype phasing simultaneously for next generation sequencing data. Phased haplotypes are estimated based on phase-informative reads which span multiple heterozygous variant sites. |
| SUGAR |
SUGAR is a java GUI software for quality check and data cleaning of ultra-high-throughput DNA sequencing data by high-resolution heatmap generation with low memory costs. |
| iSVP |
iSVP is a pipeline which applies multiple tools for detecting structural variants from NGS data in parallel and integrates the results. Currently, iSVP can be applied to deletions. In the integration, the accuracy of results varied with size of deletions from each tool is considered. (BMC Systems Biology 2013, Mimori et al.) |
| CNValloc |
CNValloc is a program to estimate sequences of alleles and copy numbers of those for each sample simultaneously at CNV loci from population-scale NGS data. The computational complexity for each step of the estimation is linearly dependent on the number of samples and the number of alleles. (BMC Bioinformatics 2015, Mimori et al.) |
| ClipCrop |
This is a tool for detecting structural variations using soft-clipping information From SAM files. |
| Cell Illustrator |
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| XiP |
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| Cell System Markup Language / Cell System Ontology |