解析ツール

Posted by: kyanobi

  1. CA_Plot_Viewer

    CA_Plot_Viewer download (Password required)

    http://bioinf.mind.meiji.ac.jp/CA_Plot_Viewer/index.php

    Contact Dr. Kentaro Yano to get the GUI software 'CA_Plot_Viewer'.

    For academic users, 'CA_Plot_Viewer' is available for free.

    For commercial users, the software is also available under a contract. Please contact Dr. Yano for utilization.

    'CA_Plot_Viewer (beta version)' assists to detect new genes with analyses of gene expression profiles and functional annotations.

    The current version of CA_Plot_Viewer can perform our developed analysis methods, based on correspondence analysis (CA), in PCs (Win, Mac, Linux etc.).

    CA_Plot_Viewer summarizes your large-scale expression data with a low-dimensional projection.

    Contact Information : Dr. Kentaro Yano (kyano_at_isc.meiji.ac.jp, please replace '_at_' by the symbol)

  2. HEAP

    Recent availability of large scale genomic resources enables us to conduct so called genome-wide association studies (GWAS) and genomic prediction (GP) studies, particularly with next-generation sequencing (NGS) data. The effectiveness of GWAS and GP depends on not only their mathematical models, but the quality and quantity of variants employed in the analysis. In NGS single nucleotide polymorphism (SNP) calling, conventional tools ideally require more reads for higher SNP sensitivity and accuracy. In this study, we aimed to develop a tool, Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both end of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html).

    Download

    Source: heap-0.8.0.tar.gz

    Docker image: centos7_heap_v0.8.0_dockerImage.tar.gz (217 MB)

    Documentation

    User manual

  3. CATchUP

    The Perl script for identification of specifically expressed genes.

    DOWNLOAD

    catchup-1.0.zip

    DATABASE

    http://plantomics.mind.meiji.ac.jp/CATchUP