The Illumina MiSeq is a compact, benchtop sequencer optimized for medium-throughput workflows, making it suitable for HuGE facility  needing flexible, targeted sequencing capabilities. Its integrated sequencing-by-synthesis chemistry and onboard optics deliver high data quality, enabling reliable detection of SNVs, indels, amplicons, and small gene panels. With a range of read-lengths and multiplexing options, MiSeq supports targeted panels, 16S metagenomics, small genome or transcriptome sequencing, and other focused applications. Its straightforward workflow, low hands-on time, and streamlined maintenance allow to process multiple runs efficiently, ensuring reproducible results across many users and experiments.