Platforms
AGRF's Next-Generation Sequencing service has the capability and experience to process sequencing projects that utilise many applications. AGRF utilises three platforms for it's next-generation sequencing projects: the Roche GS FLX, the illumina HiSeq2000 and the Life Technologies Ion Torrent PGM. 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 RNA-Seq which can be performed on the illumina HiSeq. The Ion Torrent is ideal for sequencing of small genomes, PCR resequencing, and sample confirmation for larger Next-Gen studies
Next-Generation Sequencing Service Specifications
Parameter |
GS FLX |
HiSeq2000 |
Ion Torrent PGM |
Sequencing |
300 -500 Mb per full plate run |
• Up to 35 Gbp per • Up to 70Gbp per |
>10Mbases per |
Number of |
750,000 - 1,250,000 |
300 - 400 million |
Up to 1 million |
Average |
400 bp |
• Up to 100 bp, • Up to 100 bp x 2 |
100 bp |
|
Raw Read |
>99.5 % |
>98.5 % |
>99.0 % |
Sample |
• Up to 16 regions • Barcoding options |
• 7 channels per • Up to 12 samples |
>Up to 15 |
Input |
• 1 -5 μg gDNA • 15 - 30 ug gDNA • 200 ng PCR- • 0.5 - 1 μg mRNA |
• 1 -5.0 μg gDNA • 10 - 20 μg (Mate • 200 ng PCR- • 1 - 10 μg total |
200ng of 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.
Life Technologies Ion Torrent PGM
AGRF utilises the Ion Torrent PGM platform which differs to other systems by directly detecting the sequence reaction using semiconductor technology, rather than optical sensors. This novel approach allows for much faster run times, at reduced costs. The ion torrent 314 chip can generate over 1 million reads with an average length of 100bp in under 2 hours. The expected data yields from a 314 chip are >10Mbases. AGRF utilises the “One-Touch” template preparation system for rapid processing and reproducibility, and has two PGM machines for service throughput. The AGRF's Bioinformatics team can assist with data analysis using a variety of software applications.
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