The Illumina MiSeq platform uses reversible-terminator sequencing-by-synthesis technology to provide end-to-end sequencing solutions. The MiSeq instrument is one of the smallest benchtop sequencers that can perform onboard cluster generation, amplification, genomic DNA sequencing, and data analysis, including base calling, alignment and variant calling, in a single run. It performs both single- and paired-end runs with adjustable read lengths from 1 × 36 base pairs to 2 × 300 base pairs. A single run can produce output data of up to 15 Gb in as little as 4 h of runtime and can output up to 25 M single reads and 50 M paired-end reads. Thus, MiSeq provides an ideal platform for rapid turnaround time. MiSeq is also a cost-effective tool for various analyses focused on targeted gene sequencing (amplicon sequencing and target enrichment), metagenomics, and gene expression studies. For these reasons, MiSeq has become one of the most widely used next generation sequencing platforms. Here, we provide a protocol to prepare libraries for sequencing using the MiSeq instrument and basic guidelines for analysis of output data from the MiSeq sequencing run.


NextseqNextSeq 550

The NextSeq 550 System WGS workflow offers a simple, fast, end-to-end solution for characterization of any genome. It begins with streamlined library preparation using high-quality TruSeq library preparation kits. The NextSeq 550 System’s dual density flow cell configurations and accompanying reagent kits deliver 20 Gb to 120 Gb, enabling researchers to match sequencer output with sequencing of prokaryotic and eukaryotic genomes. New v2 reagent kits are optimized to improve base calling and data quality even further.