Which Sequencing Platform Should I Choose?

At MRDNA, we pride ourselves on offering our customers the ability to choose from the latest NGS platforms the industry has to offer. But sometimes, having too many options can be confusing...where should you begin?

Ion S5 XL:

Our least expensive option is going to be the Ion S5 XL. The Ion S5 (aka PGM Sequencing Technology) is the ideal choice for probative studies...for those investigators that aren't too sure what to expect, but are curious to know what/who and how many are in their sample. The limiting factor for the Ion S5 is read length (~300-400bp). Our two most requested assays for the Ion S5 are the 515F-806R amplicon primer pair, which targets the 16s rRNA v4 region, and ITS1-ITS2 amplicon primer pair, which targets a portion of the internal transcribed spacer (ITS) region commonly used for fungal studies. Pricing for these two assays is as low as $60/assay.



The Illumina sequencing platforms are by far the most popular and arguably the most cited NGS technology. The Illumina MiSeq is able to offer read lengths up to 600bp and the Illumina NovaSeq is able to offer read lengths up to 500bp. Of course, smaller read lengths are available depending on your needs, but with longer read length capability the Illumina MiSeq and Illumina NovaSeq will be able to provide greater specificity with greater confidence than the shorter read lengths can provide. If you are interested in targeted sequencing, but maybe have an interest in regions larger than the 16s v4 region e.g. V1-3, V3-V4, or V5-V7, the Illumina MiSeq is going to be the platform for you. Pricing for targeted (amplicon) sequencing for the Illumina MiSeq begins at $85/assay but can be as low as $65/assay; pricing is dependent on project size. The Illumina NovaSeq is the definition of high-throughput sequencing. Able to generate 6TB of data and 20 Billion paired-end reads, the Illumina NovaSeq is an ideal platform for genome, metagenome, and transcriptome studies that require large amounts of data. Just as an example, bacterial genome sequencing pricing starts around $500/sample but can be as low as $350/sample; pricing dependent on project size.


PacBio Sequel:

The PacBio Sequel is a long-read sequencer that is capable of sequencing gDNA with an average insert size of 10Kb or larger. Why would you choose long-read sequencing over less-expensive platforms such as Illumina or Ion S5? Because with greater read length comes greater accuracy. With regards to targeted sequencing, such as 16s rRNA Sequencing, you're no longer limited by instrument read length capabilities to capture the gene or region of interest. From genes with size ranges spanning hundreds of bases to thousands of kilobases, SMRT Sequencing allows you to detect SNPs, indels, structural variants etc. all without sacrificing accuracy. SMRTbell sequencing technology is unique in its library construction. Where typical NGS libraries are linear, PacBio SMRTbell libraries are circular which allows the DNA polymerase to make multiple passes of the same molecule i.e. imagine driving around a race track. So again, take for instance the 16s rRNA gene, these multiple passes make it possible to achieve >99% read accuracy, and this level of read accuracy combined with the ability to sequence all 9 hypervariable regions of the 16s rRNA gene make it possible to achieve species-level identification.

Of course, SMRT Sequencing is revolutionizing Whole Genome Sequencing and RNA Sequencing. De novo genome assembly with long read sequencing is able to deliver N50 contigs in the megabases and produce reference quality assembles, and Iso-Seq analysis paired with SMRT Sequencing provides full-length cDNA sequences with no assembly required. Feel free to contact us for more pricing information.