PacBio RS II

PacBio calls their technology SMRT sequencing – single molecule, real-time. Unlike most other sequencing technologies, it doesn’t require clonal amplification of DNA – it sequences single molecules. The real-time nature of PacBio leads to three distinct advantages. First, the reads are quite fast, with runs lasting from 30 minutes to three hours (rather than days). Second, the reads are substantially longer than most other commercially available sequencing platforms (including Sanger-based sequencers), with a mean of ~15 kb. Third, the movie captures information about the rate of nucleotide incorporation, which can be used to determine the modification status of the template nucleotide (e.g. 5-mC, 5-hmC, etc.). The raw read error rate is substantially higher at around 14% compared with the 0.1 to 1% error rate of other leading systems. However, unlike the others, the error model is stochastic, so very high quality reads across all bases can be achieved in the consensus sequence. Additionally, the SMRT sequencing chemistry can sequence regions of high GC content, leading to much more uniform coverage of the genome. Given this unique mix of strengths and weaknesses, Nucleome use PacBio RS II latest chemistry for sequencing of small genomes (e.g., viral and bacterial), difficult to sequence regions or genomes (e.g., high GC content), stand alone denovo genome sequencing of larger genomes, hybrid assembly, gap filling, scaffolding, native detection of modified bases or any application where ultra long reads are necessary (e.g., full-length cDNAs).

Bionano Irys System

The Irys® System uses the patented NanoChannel Array located on the IrysChip® to linearize intact DNA for direct imaging and de novo assembly, providing the long-range genomic information required for high-resolution discovery of structural variations.\r\nIrys® NGM enables researchers to generate the highest-quality genome assemblies. Irys® NGM offers researchers in all fields the most complete and comprehensive view of genomes. The utility of Irys® NGM is virtually unlimited, providing researchers with a new set of tools for discovery, including:

 

    • Whole-genome de novo assembly

 

    • Structural variation detection

 

    • Hybrid scaffolding

 

    • Gap sizing

 

    • Haplotype phasing

 

    • Assembly validation

 

    • Quantification of repeats

 

 

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Sequel System

The Sequel is the aptly named smaller, less expensive follow-on to the RS II. The sequel can generate 5 to 7Gb data per SMRT cell. We use this instrument for de novo genome sequencing of larger genomes where the customer wants to generate higher coverage of 75X or more. But the Sequel system delivers shorter read length than PacBio RS II of lower quality, so we still recommend PacBio RSII over sequel for denovo genome sequencing programs until Sequel’s data output and quality is stabilised.

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GeneTitan

GeneTitan® Multi-Channel (MC) Instrument for expression and genotyping can be used for hybridization, washing, and imaging in a single instrument. GeneTitan® Instruments together with Affymetrix® High-Throughput (HT) Array Plates provide the hands-free, automated solution for microarray processing. With a broad selection of array plate formats, we use this instrument from discoveries through genome-wide SNP genotyping, to comprehensive explorations of gene expression profiles relating to important biological phenotypes, such as disease or drug response. We frequently use this instrument for large scale custom SNP genotyping programs using Axiom myDesign genotyping array solutions.

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HiSeq 2500

The HiSeq 2500 (1T upgrade), an upgrade of the original HiSeq 2000, has two separate operating modes, both using the standard SBS chemistry. The ‘high throughput mode’ can generate up to 1Tb per 6 days run with SBS v4 chemistry. For those willing to pay a premium for faster results, there is also a ‘rapid mode’ that is capable of generating 180 Gb in 40 hours. The new V4 reagents increase the number of clusters by 33% compared to the TruSeq SBS Kit V3, adding additional capacity for counting assays. It uses modified single-channel flow cells, onboard amplification and ‘fast’ chemistry to achieve the faster run times. We use this instrument for almost every NGS application starting from Genome, Exome, transcriptome, epigenome and Metagenome sequencing as this instrument and chemistry generates highest data quality and output.

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MiSeq

The MiSeq, which launched in the fall of 2011, is Illumina’s desktop or “personal sequencing system”. It is a smaller, faster and lower output sequencer, aimed primarily at the emerging sequencing-based diagnostics market. It is a self-contained system with onboard cluster generation, simplified reagent handling, and tight integration with Base Space, Illumina’s cloud-based data analysis platform. In November 2013 Illumina launched an FDA-cleared version of the instrument, called the MiSeqDx. Its MiSeq SBSv3 kit produces 2×300 bp read length and up to 15 Gb data in one run. We use this technology for denovo genome sequencing of smaller genomes, 16s Amplicon sequencing and sequencing of cancer panels.

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Illumina iScan

The iScan system utilises Bead-Array microarray technology for a broad range of DNA and RNA analysis applications. Each bead on Illumina arrays is covered with hundreds of thousands of copies of specific oligos ​ that act as the capture sequences in one of our array-based assays.​Bead-Array product density advancements have increased genomic coverage for whole-genome genotyping, resolution for cytogenetics and CNV detection, and sample throughput for gene expression, DNA methylation, and focused genotyping products.

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