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Next Generation Sequencing

Next Generation Sequencing (NGS) utilises massively parallel sequencing to generate thousands of megabases of sequence information per day. Our NGS service utilises the latest Illumina Sequencing Instruments including: Illumina HiSeq3000, Illumina MiSeq and Illumina HiSeq1500, providing speed, flexibility and versility for your project. We undertake both library generation and next generation sequencing.


  • Please email the facility This email address is being protected from spambots. You need JavaScript enabled to view it. requesting an initial consultation for your NGS project design
  • We also suggest that you have discussions with your bioinformatician or the Monash Bioinformatics Platform before finalising experimental design. Once the design is discussed and finalised we will email through a quotation. 

Sample submission

  • Upon quotation acceptance, please submit your samples according to our sample submission guidelines
  • All samples are submitted using this form here
  • Follow the sample submission instructions at the following link. More Info
  • We will email following quality control of your samples, library preparation, sequencing and data transfer

Data Retrieval

  • Data Retrieval is via our server using the MyTardis system
  • Times to Results is usually about 4 weeks from samples passing quality control
  • A link to your data will be provided electronically and a quality report will also be provded detailing methodologies used to enable publication. Note that links to data are valid for one month, and although we do archive data for longer, we suggest that you download and securely store your own data.

Whole genome sequencing

TruSeq® Nano DNA LT Sample Preparation Kit

TruSeq DNA PCR ­‐ Free LT Sample Preparation Kit

Exome sequencing

For Exome sequencing, we recommend 30 million reads per sample using 100 bp paired-end reads (average 60x - 100x coverage using 50 Mb target region)

Agilent SureSelect XT2 Human All Exome V5

Nimblegen SeqCap EZ Human Exome V3.0

AmpliSeq Exome

Whole transcriptome

For RNAseq gene expression studies investigating differential expression, we recommend a minimum of 30 million reads per sample using 50-100 bp fragment reads.

TruSeq® Stranded mRNA LT - poly-A enrichment

For RNAseq requiring the investigation of coding, non-coding regulation and alternative splice variants, 50-60 million reads per sample is recommended using 100 bp paired-end reads.

TruSeq® Stranded Total RNA LT -­ (with Ribo-­‐Zero Human/Mouse/Rat) - rRNA depletion

Ovation® RNA-Seq System V2 - SPIA technology

AmpliSeq Transcriptome

Total RNA that has been DNase treated (on column) needs to be supplied with a RIN score > 8 as determined by Agilent Bioanalyser analysis.

Small RNA sequencing

For Small RNA analysis, we recommend a minimum of 10 million reads per sample using 50 bp fragment reads.

TruSeq Small RNA Sample Prep Kit


For ChIP-Seq analysis, we recommend a minimum of 20 million reads per sample using 50 bp fragment reads.

Ovation® Ultralow DR Multiplex System

Methylation analysis

Zymo EZ DNA Methylation Kit