Bioinformatics Support

The Genomics Facility at Monash University Malaysia is equipped with a total of 14 Linux workstations (some up to 32 CPUs, 128 Gb RAM) to process the large amount of NGS data generated from various projects. In addition, the facility also has access into the High Performance Computing (HPC) Research Infrastructure and is collaborating closely with the team to help staff in familiarizing the system. Moreover, with affiliations to Monash University Australia, we are also granted access to the MonARCH (Monash Advanced Research Computing Hybrid), a next-generation HPC/HTC Cluster that can offer more than 1000 CPU cores to support Monash research communities. These resources provide us with the capabilities to handle a variety of projects ranging from small single gene analysis to large genome assemblies.

For bioinformatics support and collaboration, please contact us at mum.genomics@monash.edu

Bioinformatics Support

We offer a wide arrange of bioinformatics analyses to help researchers in the interpretation of their data and provide solutions to solve their research problems. The supports include:

- Next-generation sequencing data analyses (RNA-seq, Whole-genome sequencing, Exome sequencing)

- Bacterial Genome Assembly

- Bacterial Genome Annotation

- Mitochondrial Assembly

- Mitochondrial Annotation

- Metagenomics (16S, Shotgun Metagenomics)

- Phylogenetic analysis

- Microbial ANI and AAI analysis

- Pan-genome analysis

- Genomic Islands analysis

- Microbial virulence gene prediction

- Gene Clustering analysis

- SNP analysis

- Bacterial and Mitochondrial Genome NCBI submission and publication

What we do

We have developed in-house bioinformatics tools that are freely available.

MitoPhAST: an automated tool that (1) identifies annotated protein-coding gene features and generates a standardised, concatenated and partitioned amino acid alignment directly from complete/partial GenBank/EMBL-format mitogenome flat files, (2) generates a maximum likelihood phylogenetic tree using optimised protein models and (3) reports various mitochondrial genes and sequence information in a table format. MitoPhAST is available for download at: https://github.com/mht85/MitoPhAST

Since the start of the Genomics Facility in 2013, we have undertaken a variety of projects which require different sets of skills and programs.

Below are some examples of the programs we use, switching between Windows OS and also Linux OS

Sequence read QC

Genome assembly and annotation

Transcriptomics and RNA-seq analysis

Mitogenome assembly and annotation

Metagenomics

Microsatellite detection and primer design

Phylogenetic analysis

Giving back to Monash

In addition to providing bioinformatics services, we truly believe in empowering the students and staff of Monash University Malaysia with the skills and knowledge required to conduct various NGS analysis for their own projects. To do so, an additional Linux workstation (16 CPUs, 64 Gb RAM) with a licensed CLC Genomics Workbench software has been set up for shared use (please contact us for more information on getting access to the workstation). We have also successfully conducted several NGS workshops with more to come. In the mean time, we welcome students and staff alike to drop by the office with any questions and queries regarding NGS, its applications and analysis.