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Installed Software

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The following scientific applications, programming tools and libraries, among others, are already installed on CGS-HPCF cluster. Please refer to the CGS-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

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

Impute

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


Sequence Analysis & Next-Generation Sequencing Software

ABySS

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.

BWA

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.

Samtools

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

VCFtools

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

Bowtie

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

Cufflinks

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

 

Programming Tools and Libraries

BioPerl

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

R

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.

 

Contact

  Mr Kelvin Wong
  Mr Juilian Yeung
  Ms Eunice Cheung

 




  Telephone: 2831 5436 / 2831 5147 / 2831 5438
  Email: itsupport.cgs@hku.hk