The Illumina MiSeq sequencer allows you to access more focused applications such as targeted gene sequencing, metagenomics, small genome sequencing, targeted gene expression, amplicon sequencing, and HLA typing. The MiSeq is capable of delivering up to 15 Gb of output with 25 million sequencing reads and 2x300 basepair read lengths.
The Ion GeneStudio S5 System is a semiconductor-based that enables the production of high-quality sequencing data and allows you to go from DNA library to data in as little as 24 hours with only 45 minutes of total hands-on time when paired with the Ion Chef System. The Ion GeneStudio S5 System is optimized for simple targeted sequencing workflows and you can use as little as 1 ng input DNA or RNA. You can achieve from 2-80 million reads per run depending on the chip you select.
The Oxford Nanopore MinION allows for long read lengths and is suitable for projects including but not limited to the following: WGS, Metagenomics, Targeted Sequencing, Whole transcriptome (cDNA), Smaller transcriptomes (direct RNA), and multiplexing for smaller samples. The MinION yields up to 50 Gb of data per flow cell. A benefit of the MinION system is that flow cells may be re-used, making it cost effective.