DDBJ Database updates and computational infrastructure enhancement

Abstract

The Bioinformation and DDBJ Center (https://www.ddbj.nig.ac.jp) in the National Institute of Genetics (NIG) maintains a primary nucleotide sequence database as a member of the International Nucleotide Sequence Database Collaboration (INSDC) in partnership with the US National Center for Biotechnology Information and the European Bioinformatics Institute. The NIG operates the NIG supercomputer as a computational basis for the construction of DDBJ databases and as a large-scale computational resource for Japanese biologists and medical researchers. In order to accommodate the rapidly growing amount of deoxyribonucleic acid (DNA) nucleotide sequence data, NIG replaced its supercomputer system, which is designed for big data analysis of genome data, in early 2019. The new system is equipped with 30 PB of DNA data archiving storage; large-scale parallel distributed file systems (13.8 PB in total) and 1.1 PFLOPS computation nodes and graphics processing units (GPUs). Moreover, as a starting point of developing multi-cloud infrastructure of bioinformatics, we have also installed an automatic file transfer system that allows users to prevent data lock-in and to achieve cost/performance balance by exploiting the most suitable environment from among the supercomputer and public clouds for different workloads.

SPDB: a specialized database and web-based analysis platform for swine pathogens

“…As a management system, 26 148 genome sequences of swine, bacterial pathogens, viral pathogens, parasitic pathogens and phage were collected, which are searchable in three modes using 17 fields. The SPDB genome search tool offers many advantages over the widely used sequence databases, such as NCBI ( 20 ), DDBJ ( 21 ), EMBL-ENA ( 22 ) and other pathogen-specific sequence databases ( 10 , 23 , 24 ). Firstly, compared with the other databases that only provide the English version, the SPDB is available in both English and Chinese, which is beneficial to the vast number of users whose native language is Chinese.…”

“…However, the application of NGS in swine disease research has several limitations in the context of data, including data storage, management and maintenance. Currently, the most common data management systems used for swine pathogen sequences are the National Center for Biotechnology Information (NCBI) ( 20 ), DNA Database of Japan (DDBJ) ( 21 ) and the European Nucleotide Archive (EMBL-ENA) ( 22 ). However, information retrieval is relatively complex and inconsistent among these resources.…”

Practical guide for managing large-scale human genome data in research

“…It supports SIF images as well as Docker images. It only requires user privileges and therefore some HPC systems have better support for Singularity, e.g., NIG [52]. Finally, a container registry, e.g., DockerHub (https://hub.docker.…”

Ten simple rules for annotating sequencing experiments

“…The National Center for Biotechnology Information database of Genotypes and Phenotypes (NCBI dbGAP) [28] and the European Genome-phenome Archive (EGA) [29] resources specialize in permanent archiving and sharing of personally identifiable genetic and phenotypic data resulting from biomedical research projects including sequencing data. For data that are not personally identifiable, the NCBI SRA [30], the European Nucleotide Archive (ENA) [31], and the DNA Databank of Japan [32] make biological sequence data available to the research community. GEO [33] and BioSamples [34] collect mainly metadata and references to the respective sequencing data in other databases.…”