Laboratory of Medical Microbiology

Next-Generation Sequencing

Next-Generation Sequencing

The LMM houses both second and third generation sequencers in a spacious room with dedicated space for DNA/RNA isolation and quantification.

In addition, the following equipment are readily available:

  • PacBio Sequel systems both for fulfilling in-house and third-party sequencing requirements.
  • Several thermal cyclers (PCR) and qPCR devices (Applied Biosystem and BioRad)
  • Bioanalyzer (Agilent)
  • Lab Chip (Perkin Elmer)
  • Zephyr G3 (Perkin Elmer)
  • MiSeq (Illumina Inc.)
  • MinION (Oxford Nanopore)

The LMM can provide instruments for quantity and quality control and a Zephyr G3 NGS automatic sample handling system robot that facilitates high-throughput library preparation.

Hercules: Pacbio Sequel

Single molecule long-read sequencing technology: beyond state-of-the-art in biological and medical research (01/05/2018 -30/04/2021)

Whole Genome Sequencing

With a variety of sequencing instruments available at the LMM, we have the expertise in providing services in whole genome sequencing. We have developed a whole genome sequencing analysis pipeline for bacterial genomes named BacPipe which is pending publication and will be made open-access when published.

BacPipe is capable of performing de novo and hybrid genome assemblies combining long-read sequencing with short-read Illumina data to close the gaps in the genome assemblies generated by short-read sequences and identify mis-assemblies.

MinION and PacBio Sequel can be utilised to obtain complete chromosomes, including plasmids, plastids, and mitochondrial sequences. PacBio can also be used to determine epigenetic modifications (methylation), targeted sequencing, and detect isoforms.

The LMM has the capability of conducting metagenomics analysis for microbial composition and taxonomical diversity by 16SrDNA, Internal Transcribe Spacer (ITS), and by shotgun sequencing.