Home High-Performance Computing Facility Installed Software

Installed Software


The following scientific applications, programming tools and libraries, among others, are already installed on HPCF cluster. Please refer to the HPCF user guide in wiki for more information of the available software.

Should you have suggested genomics or bioinformatics software for system-wide use, please feel free to advise us with the software details.


Genome-wide Association Study Software


PLINK is whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.


IMPUTE is a program for estimating ("imputing") unobserved genotypes in SNP association studies.

Sequence Analysis & Next-Generation Sequencing Software


ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The parallel version is implemented using MPI and is capable of assembling larger genomes.


Burrows-Wheeler Alignment (BWA) is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. BWA excels in its speed. Mapping 2 million high-quality 35bp short reads against the human genome can be done in 20 minutes.


SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.


It can be used to perform common tasks with VCF files such as file validation, file merging, intersecting, complements, etc.


Align short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour.


Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples


Programming Tools and Libraries


BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.


R is an open source programming language and software environment for statistical computing and graphics. The R language is widely used among statisticians for developing statistical software and data analysis.



  Mr Kevin Tsang
  Ms Eunice Cheung
  Mr Juilian Yeung
  Mr Louis Lai

  Telephone: 2831 5417
  Email: itsupport.cpos@hku.hk