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Platforms

 

AGRF's Next-Generation Sequencing service has the capability and experience to process sequencing projects that utilise many applications. AGRF utilises two platforms for it's next-generation sequencing projects: the Roche GS FLX and the illumina GA II. The GS FLX generates longer read lengths for applications including de novo genome sequencing and re-sequencing. Applications that use short reads, but require greater sequencing depth, include ChIP-Seq which can be performed on the illumina GA II.


Next-Generation Sequencing Service Specifications

  Parameter

  Roche GS FLX (454)

  Illumina HiSeq2000

  Sequencing output

  300 -500 Mb per full
  plate run

  • Up to 35 Gbp per full run
     (single read)

  • Up to 70Gbp per full run
     (paired end)

  Number of Reads

  750,000 - 1,250,000 per
  full plate run

  300 - 400 million per full run

  Average Read
  length

  400 bp

  • Up to 100 bp,

  • Up to 100 bp x 2
     (Paired end)

  Raw Read
  Accuracy

  >99.5 %

  >98.5

  Sample Options

  • Up to 16 regions per
     plate

  • Barcoding options
     available

  • 7 channels per flow cell

  • Up to 12 samples per
     channel

  Input
  Requirements

  • 1 -5 μg gDNA
     (shotgun)

  • 15 - 30 ug gDNA
     (paired-end)

  • 200 ng PCR-generated
     template

  • 0.5 - 1 μg mRNA

  • 1 -5.0 μg gDNA (single and
     paired end reads)

  • 10 - 20 μg (Mate Pair Reads)

  • 200 ng PCR-generated
     template

  • 1 - 10 μg total RNA

  • >20 ng ChIP DNA

Roche GS FLX

AGRF utilises the Roche GS FLX sequencing platform, providing unparalleled read capacity with state-of-the-art sequencing technology.  Many applications have been developed for this instrument, including the large scale analysis of bacterial/yeast genomes, BAC pools, transcriptomes, microRNA libraries and ultra deep Amplicon sequencing.  In addition, the new application of paired-end sequencing enables contig alignment, greatly reducing the time for bacterial/yeast genome finishing.  The GS FLX is capable of producing up to 1,250,000 reads per run with an average read length between 200 and 400 bp or up to 500 Mb total sequence at 99.5% raw base accuracy.  The AGRF's Bioinformatics team utilises leading sequence analysis software enabling high quality base calling and flexibility to accommodate a variety of applications.


illumina HiSeq2000

AGRF utilises the illumina HiSeq2000™ platform which uses a massively parallel sequencing-by-synthesis approach to generate billions of bases of high-quality DNA sequence per run. Many applications have been developed for this instrument, including RNA Sequencing, and ChIP-Seq. The HiSeq 2000 produces an output of up to 400, 000, 000 reads per 1 lane run with an average read length of up to 100 bp or >70 Gbp total sequence. The AGRF's Bioinformatics team use leading sequence analysis software enabling high quality base calling and flexibility to accommodate a variety of applications.


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