A capillary-based fluid handling system, the ACAPELLA-5K (A5K), has been developed to prepare precise mixtures of sample and reagents in glass capillaries at a rate of 5000 preparations in 8 hours. Following a user-defined protocol the system architecture enables sample aspiration, reagent dispensing, mixing, and thermal cycling, with intermediate imaging steps for in-process monitoring of critical fluid delivery steps. A serial pipeline process is used to provide flexibility, reproducibility, and reliability for the reactions prepared. A typical reaction comprises a 0.5 μL sample aspirated from a microplate well followed by 1 to 8 reagents dispensed in 40-100 pL droplet volumes using piezoelectric reagent dispensers. Reactions are then mixed to prepare a 2.0 μL final reaction volume. Reaction volumes from 0.5-2 μL have been demonstrated, representing performance comparable to the state-of-the-art in a majority of core sequencing facilities. A5K has been extensively tested in the preparation of deoxyribonucleic acid (DNA) polymerase chain reaction (PCR) and DNA sequencing reactions. Other applications of the A5K platform of technologies include quantitation of minimal residual disease, protein crystallography, and potential for application in drug discovery, forensics, and DNA analysis of environmental samples.