Research
SCELSE Sequencing Capacity

SCELSE’s sequencing facility is designed to provide its researchers and collaborators access to cutting-edge, next-generation sequencing technologies. SCELSE’s current sequencing capacity consists of three Illumina HiSeqX instruments (owned by MedGenome Labs Pvt. Ltd.), two Illumina HiSeq2500 platforms, two Illumina MiSeq sequencers and a Pacific Biosciences RSII single-molecule sequencer. SCELSE has received the first three HiSeqX instruments in Singapore, which are super high-throughput sequencers that can each produce more than 2 terabases of data per run (2.5 days), and are designed for whole human genome sequencing. The HiSeq2500 can be run in two different modes, a rapid and a high-output mode. It allows for massively parallel sequencing and generates up to 6 billion reads in the high-output mode at a read length of up to 100bp or up to 1.2 billion reads in the rapid mode at a read length of up to 250bp. The following applications are currently supported on the HiSeq2500 platform:

  • whole genome sequencing
  • RNA-seq: transcriptome sequencing (including strand-specific libraries)
  • de novo sequencing 
  • metagenomic sequencing of complex environmental samples
  • targeted enrichment (sequence capture)
  • sequencing of mate-pair libraries
  • single-read or paired-end sequencing
  • multiplexed (barcoded) sequencing

 

The MiSeq sequencer is a smaller desktop platform that allows researchers to go from sample to data in as little as one day. At a read length of up to 300bp, the MiSeq generates up to 10Gb of data, or ~30 million reads. Applications currently supported on the MiSeq platform include:

  • small genome sequencing
  • RNA-seq: transcriptome sequencing (including strand-specific libraries)
  • small RNA sequencing
  • amplicon sequencing
  • genome resequencing
  • de novo sequencing 
  • ChIP-Seq
  • library QC
  • targeted enrichment (sequence capture)
  • single-read or paired-end sequencing 
  • multiplexed (barcoded) sequencing

In addition to the Illumina sequencers, the facility also has a Pacific Biosciences RSII single-molecule sequencer that produces very long sequencing reads (>15kb). This platform is ideal for de novo sequencing of microbial or other smaller genomes.

Preparation of next-generation sequencing libraries for various applications is supported by a robust framework of other lab instruments such as the Covaris S220 and E220, Bioanalyzer 2100, Fragment Analyzer, QuantiFluor fluorometer, Pippin Prep and Blue Pippin, and a ViiA-7 qPCR machine. SCELSE has also incorporated state-of-the-art robotic liquid handlers into its pipeline to allow for high-throughput sample processing. In addition, the Centre is continuously improving existing protocols and establishing new protocols to enable processing of even the most challenging of samples, such as low-input or environmental samples. A Laboratory Information Management System (LIMS) is used to evaluate projects and track the workflow of the different services that SCELSE provides and also enables the users to track the status of their projects and requests online.

SCELSE has closely integrated expertise in computational biology such as bioinformatics, biostatistics, and systems biology into its facility in order to optimize throughput, data handling, and analyses of the massively parallel data sets and also to provide a crucial bridge between the experimental platform and the users. SCELSE’s bioinformatics team uses in-house tools as well as commercially available software for sequencing data analysis. The Centre’s work is currently supported by an in-house computer cluster consisting of 2,720 CPU-cores, 7.8 TB RAM and a 1 PB storage array.

SCELSE works closely with sequencing-related companies to ensure continuous access to the latest technologies and sequencing products to stay abreast of the rapidly evolving technology associated with massively parallel sequencing.

 

For enquiries regarding the SCELSE sequencing facility, please contact Dr Daniela Moses at danielamoses@pmail.ntu.edu.sg