Services
– NGS
NGS Service Providers
The 'gravitational center' of the NGS universe may be shifting away from Illlumina. For instance, AVITI and PacBio platforms offer significant advantages over Illumina platforms, as each company discussed at their LSU presentations in March 2023. These companies are also committed to assisting researchers with the entire process of generating scientific results... from project design to library construction to bioinformatic analysis.
You can learn more about these options through the links below. Finally, the LSU Genomics Core will be happy to connect you to the AVITI or PacBio representatives for further information, project assistance, and service providers.
AVITI (Element Biosciences)
The AVITI platform is a 'short-read' sequencer, with support coming this year for 2X300 paired-end reads. However, while Illumina still relies on SBS (sequencing by synthesis) methodology, Element Biosciences takes a completely different approach – Avidity chemistry. While simultaneously reducing sequencing costs, the use of avidites with coiled polytomies of rolling-circle replicated templates:
– dramatically enhances the signal:noise ratio;
– permits unbiased sequencing of GC-rich regions;
– maintains register even after long homopolymers;
– minimizes bias for short reads in normally-distributed libraries;
– nearly eliminates index-hopping;
– dramatically reduces error rates overall; and,
– reduces the level of coverage required.
Libraries can be contructed by a plethora of 3rd party kits. Then, researchers can choose from two simple workflows to convert the libraries (without PCR) for processing on the AVITI platform.
Finally, with LoopSeq kits, the AVITI platform can generate synthetic long-reads from large templates. For example, this technology allows for metagenomics using full-length 16S reads as well as RNA analyses from full-length transcripts. LoopSeq can also be used to replace long-read Sanger-Sequencing in high throughput situations.
PacBio (Pacific Biosciences)
When ultra-long reads (up to 25-kb) are needed, it's definitely time to consider PacBio. This company's platforms originally had high error rates, but HiFi sequencing methodolgy has driven error rates down sharply (e.g., 8 incorrect nts in a 19-kb template).
Even with templates much shorter than 25-kb (such as metagenomics and RNA-seq), PacBio's long-read technology can greatly simplify the bioinformatics and deliver more information. Further, new kits allow for greater efficiencies by concatenating multiple 'short' (e.g., 1.5 kb) fragments into one long template. Each of the original templates remains identifiable (for bioinformatics) through the addition of indexes in the concatenation process.
Finally, PacBio's chemistry has other benefits beyond "long reads". For instance, because PacBio can monitor the kinetics of base incorporation, it can detect methylation of native DNA (without bisulfite-treatment). Thus, with 5-base HiFi sequencing, the same sequencing library can reveal SNVs, indels, and SVs as well as identify genome-wide methylation patterns associated with gene activity and other biological functions. Further, long HiFi reads enable phasing of the genetic and epigenetic variants into parental haplotypes.
In-House NGS (Ion Torrent S5)
The Ion Torrent S5 was acquired by the Core in early 2016. Prior to beginning a project destined for the S5, please contact us to discuss options and requirements for a successful run. Depending on the chip and kits used, final reads from a single run range from ~20-30 million (up to 400bp) or ~60-80 million reads (up to 200bp). Further details on this platform are provided at Ion Torrent S5 services.
In-House Services for NGS Libraries
NGS library construction is typically performed by the researcher's laboratory; however, the LSU Genomics Core provides a variety of services related to library preparation and QC.
Request Instrument Acquisition
Are you interested in having a new NGS platform available "in your backyard"... the LSU Genomics Core? If so, please email the Genomics Core, outlining why you would like to see that platform physically available here. Some helpful issues to include are: