Software

Refer to the links for each software for detailed usage instructions.

Job Scheduler

A job scheduler automatically allocates computational resources (CPU cores and memory) to each user in an environment where many users share cluster computers.

Name	2019 System		2025 System
	General Analysis Division	Personal Genome Analysis Division	General Analysis Division	Personal Genome Analysis Division
Grid Engine	Installed	Requires Application	☓	(Requires Application)
Slurm	☓	Requires Application	Installed	Installed

Package Managers

The following package managers can be used with user permissions only, making it easier to set up development and analysis environments.

Name	2019 System		2025 System
	General Analysis Division	Personal Genome Analysis Division	General Analysis Division	Personal Genome Analysis Division
Environmental Modules	X	X (CentOS 7 environment only)	X	X
Spack	Available	Available	Available	Available

Container

Name	2019 System		2025 System
	General Analysis Division	Personal Genome Analysis Division	General Analysis Division	Personal Genome Analysis Division
Apptainer (formerly Singularity)	Installed	Installed	Installed	Installed
Singularity CE (formerly Singularity)	Installed	Installed	Installed	Installed
BioContainers Apptainer (formerly Singularity) Images	Installed	Installed	Installed	Installed

Analysis Pipeline

Name	2019 System		2025 System
	General Analysis Division	Personal Genome Analysis Division	General Analysis Division	Personal Genome Analysis Division
DFAST	Available	Available	Available	Available
TogoImputation (beta)	Unavailable (Demo feature in preparation)	Requires Application	Unavailable (Demo feature in preparation)	Requires Application
NVIDIA Parabricks	☓	Installed	☓	Installed
Rhelixa RNAseq Pipeline	Installed	Requires Application	Installed	Requires Application

Data Transfer & Sharing

Archaea tools and Aspera are software suitable for large-scale long-distance data transfers compared to scp, sftp, and ftp.

Name	2019 System		2025 System
	General Analysis Division	Personal Genome Analysis Division	General Analysis Division	Personal Genome Analysis Division
Archaea tools (formerly HCPtools) Server	☓	Installed	Installed	Installed
Archaea tools (formerly HCPtools) Client	Available	Available	Available	Available
Aspera Server	Installed	☓	☓ (Installed in the DDBJ business division)	X (Installed in the DDBJ business division)
Aspera Client	Available	Available	Available	Available
scp, sftp, ftp (Client)	Installed	Installed	Installed	Installed

Development Environment & Libraries

Most development environments are pre-installed in the system. For specific versions needed for reproducibility of analyses, users can (1) install from tarball themselves, (2) use package managers available with user permissions, or (3) use Singularity containers.

Name	General Analysis Division		Personal Genome Analysis Division
	General Analysis Division	Personal Genome Analysis Division	General Analysis Division	Personal Genome Analysis Division
Python	Available	Available	Installed	Installed
R	Available	Available	Installed	Installed
Jupyter Notebook	Available	Available	Available	Available
Jupyter Lab	Available	Available	Available	Available
R Studio Server	Available	Available	Available	Available
Java	Available	Available	Available	Available
Node.JS, TypeScript	Available	Available	Available	Available
Rust	Available	Available	Available	Available
C/C++ (GCC)	Installed	Installed	Installed	Installed
AMD Optimizing C/C++ and Fortran Compilers (AOCC)	Installed	☓	Installed	Installed
C/C++ (Intel Compiler)	Installed	☓	Installed	☓
C/C++ (PGI Compiler)	Installed	☓	Installed	☓
CUDA	Installed	Installed	Installed	Installed
Go	Available	Available	Available	Available