Choosing a Sequencing Platform
With all of the recent advances in genomic data analysis, it is worth examining where the raw sequence data actually comes from. Researchers have a few choices of sequencing platforms, from (1) low-throughput Sanger sequencing to (2) innovative next-gen sequencing (aka NGS sequencing) and (3) third-generation sequencing technologies (aka long-read sequencing). Platform choice will depend on the scale of the project, the cost of sequencing, and the ultimate research question being answered by downstream analysis.
Nature Methods selected long-read sequencing as their 2022 “Method of the Year.” Several companies made innovations in the long-read sequencing space last year, improving accuracy and reducing cost. If you’re wanting to do whole genome sequencing in order to look for rare variants, long-read sequencing platforms are the best choice to simplify downstream genome assembly and analysis.
PacBio: “Traditional” Long-Read Sequencing
PacBio HiFi sequencing is one of a few choices for long-read sequencing (10,000+ base pairs per read), as opposed to older methods that were all primarily short-read (50-300 base pairs). It is very time and labor-intensive to assemble short reads correctly, and if the genome is from an organism that lacks a high-quality reference genome or has many repeat sequences or rare variants, it makes assembly even more challenging and less accurate.
Long-read technology, on the other hand, produces reads over 10,000 base pairs in length. This has the dramatic advantage of faster and easier genome assembly as well as higher accuracy in identifying rare variants and distinguishing repeating sequences more clearly. PacBio HiFi sequencing has an accuracy rate of over 99% and was the sequencing technology of choice for the recently completed Telomere-to-Telomere project to complete the human genome sequence. In 2022, PacBio introduced its new Revio platform, with higher throughput and much lower cost.
Oxford Nanopore: A Novel Sequencing Method
Nanopore sequencing is a relatively new technology, standing in contrast to established “sequencing-by-synthesis” methods. DNA is passed through a protein nanopore with an electric current. Each of the four bases in DNA causes a unique disruption in that current, which can be measured and translated into the respective base. Nanopore sequencing is beginning to be widely used, but its accuracy can range from 87-98%, making it challenging to use for the identification of rare SNPs, for example. However, the accuracy is constantly improving.
Illumina Sequencing: Moving from Short to Long Read
Illumina is the latest major sequencing company to announce a new platform, utilizing new chemistry for faster sequencing that will also be compatible with their move into long-read sequencing. In a press release, Illumina touted a redesign of almost all major elements of their previous NovaSeq 6000 platform. They launched a “fundamentally new” form of sequencing by synthesis chemistry called XLEAP-SBS which is twice as fast and up to three times more accurate than their previous method.
Interestingly, Illumina has also introduced 15 new reagents that are stable at room temperature, lowering shipping costs and reducing the need for cold shipping. The new sequencing chemistry will not be compatible with their existing NovaSeq 6000 but will be compatible with their new Infinity protocol for long-read sequencing. For a company so well-established in the short-read sequencing space, its move into long-read sequencing is telling of its promise.
Outsourcing Bioinformatics Analysis: How Bridge Informatics Can Help
Many of our clients at Bridge Informatics are at the cutting edge of research, using sophisticated bioinformatics tools to tackle their research questions. From pipeline development and software engineering to deploying existing bioinformatics tools, Bridge Informatics can help you on every step of your research journey.
As experts across data types from leading sequencing platforms, we can help you tackle the challenging computational tasks of storing, analyzing, and interpreting genomic and transcriptomic data. Bridge Informatics’ bioinformaticians are trained bench biologists, so they understand the biological questions driving your computational analysis. Click here to schedule a free introductory call with a member of our team.
Jane Cook, Biochemist & Content Writer, Bridge Informatics
Jane Cook, the leading Content Writer for Bridge Informatics, has written over 100 articles on the latest topics and trends for the bioinformatics community. Jane’s broad and deep interdisciplinary molecular biology experience spans developing biochemistry assays to genomics. Prior to joining Bridge, Jane held research assistant roles in biochemistry research labs across a variety of therapeutic areas. While obtaining her B.A. in Biochemistry from Trinity College in Dublin, Ireland, Jane also studied journalism at New York University’s Arthur L. Carter Journalism Institute. As a native Texan, she embraces any challenge that comes her way. Jane hails from Dallas but returns to Ireland any and every chance she gets. If you’re interested in reaching out, please email [email protected] or [email protected].