Massive Parallel Sequencing

 

iontorrent illumina roche454

VIB Nucleomics Core offers a wide variety of Next Generation Sequencing platforms, with great flexibility in running both small and large scale projects within a reasonable time.

 

Overview of the available sequencing equipment and their capacity

 

Instrument Time Read length Lanes Max # reads Max cap.
Roche GS-FLX 10 h 500 bp 2/4/8/16 106 500 Mbp
Roche GS-Junior 10 h 500 bp 1 70*103 35 Mbp
Illumina HiSeq* 14 days 1*35 – 2*100 bp 2*8 3*109 > 600 Gbp
Illumina MiSeq 4-27 h 1*35 – 2*150 bp 1 3,4*106 > 1 Gbp
Ion Torrent PGM > 30 min 200 bp (soon 400) 1 105 (314 chip)
106 (316 chip)		 10 Mbp
100 Mbp

* Offered through subcontracting the sequencing run

Most appropriate applications

 

illumina miseq

Illumina

  • genome sequencing (not MiSeq)
  • exome sequencing (not MiSeq)
  • digital gene expression (not MiSeq)
  • transcriptomics (small transcriptomes on MiSeq)
  • small RNA sequencing
  • ChIP-Seq
  • targeted resequencing
  • MiSeq: QC for HiSeq libraries

 

Roche 454

  • small genomes
  • targeted resequencing
  • metagenomics
  • transcriptomics
  • Junior: QC of FLX libraries
roche 454

 

ion torrent

Ion Torrent

  • targeted capture
  • targeted amplicon
  • small genomes
  • miRNA
  • ChIP-Seq sequencing library
  • QC Genome/exome validation

 

 

Steps

Steps in each sequencing project, irrespective of the platform or application:

  1. library preparation
  2. amplification: emulsion PCR (Roche 454 and IonTorrent) or bridge amplification (Illumina)
  3. the sequencing itself

 

Sequencing library preparation

The sequencing library preparation is highly dependent on the application and often multiple vendors are offering slightly different library preparation kits. VIB Nucleomics Core is constantly implementing these library preparation protocols, preferentially on an automated platform. Especially with targeted resequencing, many options are available to enrich for sequences of interest to the researcher. PCR based approaches are very well suited for the smaller target regions (< 200 kbp).

Companies offering PCR based enrichment solutions:

 

Sequencing capacity

The sequencing capacity of the GS Junior, IonTorrent, and MiSeq fit very well with required coverage of smaller-sized target regions. Larger target regions, such as whole exomes, benefit more from hybridization based enrichment. Those experiments will need the sequencing capacity from GS-FLX or HiSeq.

Companies offering hybridization based enrichment:

 

Outsourcing

Apart from running sequencing services in-house on 454, IonTorrent or Illumina, VIB Nucleomics Core, through its contacts with other service providers, also can offer project management involving outsourcing to established companies like Complete Genomics, BGI or for evaluation to technology providers building novel platforms (e.g. nanopore technology or Pacific Biosciences).

 

Experimental design, sample requirements, and data analysis expectations

Clearly, sequencing is currently a rapidly evolving field with already now a wealth of different applications and options to the researcher.   Therefore we highly recommend to contact us and to consult us on experimental design, sample requirements, and data analysis expectations.

Sample submission