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	General Analysis Division	Personal Genome Analysis Division
Slurm	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	General Analysis Division	Personal Genome Analysis Division
Spack	Available	Available

Container

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

Analysis Pipeline

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

Commercial analytics pipeline

Name	General Analysis Division	Personal Genome Analysis Division
NVIDIA Parabricks	☓	Installed
sentieon	☓	Installed
NVIDIA AI Enterprise	☓	Installed

Data Transfer & Sharing

Aspera and Archaea are software tools optimized for large-scale data transfers over long distances, offering advantages over protocols like SCP, SFTP, and FTP.

• Aspera can be used to download data from sources such as NCBI, EBI, and DDBJ to supercomputers or users' personal computers. (Up to a total bandwidth of 10 Gbps)
• Archaea tools are available for transferring data between the user's home directory on the supercomputer and their personal computer. (No bandwidth limit)

For more details, please refer to:

• Data file transfer（The general analysis division）
• Data file transfer（The Personal Genome Analysis division）

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

Commercial Compiler

Name	General Analysis Division	Personal Genome Analysis Division
C/C++ (Intel Compiler)	Installed	☓
AMD Optimizing C/C++ and Fortran Compilers (AOCC)	Installed	Installed
C/C++ (PGI Compiler)	Installed	☓