Understanding MiSeq VS HiSeq

August 12, 2022

What Are MiSeq and HiSeq?

Genetic sequencing powerhouse Illumina has developed a huge variety of sequencing platforms to choose from, all with different capacities and applications. Selecting the most appropriate sequencing platform depends on the type of study you are performing, and if short-read sequencing is your method of choice, two of the leading choices are the MiSeq and HiSeq platforms.

The HiSeq platform is a high-throughput platform that has the unique feature of switching between a rapid output mode and a higher output but slightly slower mode, depending on the size of the study. HiSeq runs produce paired-end reads of around 250 bp. However, this platform has recently been discontinued by Illumina, and will only be supported through 2023.

For current and future applications, MiSeq will go from HiSeq’s competitor to its successor. The MiSeq system comes with pre-optimized library preparation kits depending on the type of study, and combines the rapid output capacity of HiSeq with slightly longer paired-end 300 base pair reads. This more streamlined approach, both faster and higher output, makes MiSeq an advantageous choice for high-throughput studies.

Applications of Short-Read Sequencing

So why use Illumina, and specifically MiSeq? For targeted sequencing analyses, for example when the gene(s) of interest are well-established in reference genomes already, a short-read approach can be faster and more cost-effective than whole genome or long-read sequencing.

Outsourcing Bioinformatics Analysis

However, storing and interpreting this raw sequence data is a challenging computational task. At Bridge Informatics, our experts can help design custom cloud infrastructure and robust analytical pipelines for your genomic analysis. Book a free discovery call with us to discuss your project needs.

Jane Cook, Journalist & Content Writer, Bridge Informatics

Jane is a Content Writer at Bridge Informatics, a professional services firm that helps biotech customers implement advanced techniques in management and analysis of genomic data. Bridge Informatics focuses on data mining, machine learning, and various bioinformatic techniques to discover biomarkers and companion diagnostics. If you’re interested in reaching out, please email daniel.dacey@old.bridgeinformatics.com or dan.ryder@old.bridgeinformatics.com.




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