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.

Package Managers

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

Container

Analysis Pipeline

Commercial analytics pipeline

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 EBI and DDBJ to supercomputers or users' personal computers. (Up to a total bandwidth of 10 Gbps)
  • Currently, Aspera is not available at NCBI; use of the SRA-toolkit is recommended.
• 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）

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.

Commercial Compiler

Commercial Python Libraries