Difference between MiSeq and MiniSeq

Summary of this article

The MiSeq and MiniSeq are Illumina's next-generation sequencers that can be used for different applications and data throughputs: the MiSeq is suitable for medium-scale projects and in-depth analysis, while the MiniSeq is a cost-effective model for smaller targeted sequencing. You can choose the appropriate sequencer for your application and data throughput.

1. Data Throughput

MiSeq：
Data throughput can generate up to 15 Gb of data.This allows for medium to slightly larger projects (e.g., whole genome sequencing and gene expression analysis).
In addition, paired-end reads can be sequenced up to 300 base pairs (300 bp × 2 reads ), allowing detailed analysis using long reads. This is important because the ability to read up to 300 bp is necessary when measuring STRs.
MiniSeq：
Data throughput is up to 7.5 Gb, about half that of MiSeq. This is primarily suited for small targeted sequencing and analysis of limited regions.
MiniSeq provides up to 150 base pairs (150 bp × 2 reads) of paired-end reads and is limited to sequencing shorter reads than MiSeq.

2. Application Flexibility

MiSeq：
It has a wide range of applications and can be used for a variety of applications, including small-scale targeted sequencing, medium-scale whole genome sequencing, 16S rRNA analysis, RNA sequencing, and microbial genome analysis. It is especially suitable for medium-scale projects and studies requiring more detailed sequencing.
MiniSeq：
It is designed primarily for targeted sequencing and small-scale gene expression analysis, making it somewhat limited in its applications. Designed for small data volumes and read lengths, it is not suitable for projects requiring extensive sequencing or high throughput. MiniSeq is cost-effective and specifically designed for smaller projects.

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3. Installation and Operation of Equipment

MiSeq：
As a sequencer for generating more data, the MiSeq also requires slightly more installation space and power consumption. It is suitable for medium to large laboratory and clinical projects.
MiniSeq：
The MiniSeq is designed as a compact and easy-to-operate model. It is suitable for laboratories with limited space or small projects.

summary

MiSeq offers higher data throughput and longer read lengths, and its breadth of applications makes it suitable for medium-scale genome analysis and complex projects.
MiniSeq is ideal for small projects with low data volumes and for targeted sequencing that requires easy and cost-effective sequencing.

Thus, the large data throughput and the range of analytical applications are the biggest differences between the MiSeq and MiniSeq.