ABSTRACT
This chapter focuses on sequencing the prepared libraries using the MiSeq FGx or Ion series instruments. The MiSeq requires the user to supply only the reagent cartridge, a plastic casing with multiple wells each prefilled with the necessary sequencing reagents, flow cell to sequence pooled, normalized libraries, and a waste bottle. The reagent cartridges and flow cells can only be purchased from Verogen for forensic use while the same from Illumina can be used for research use only (RUO) mode applications. The flow cell is removed from the buffer-containing vial which is shipped in, and wiped dry with care with laboratory wipes to remove all streaks before placing it in its holder in the instrument to click it into place. The instrument records its barcode and checks that the flowcell is unused and not expired. A new run is created in the Verogen Universal Analysis Software (UAS) prior to beginning the sequencing run.
