Abstract: Methods and systems for analysis of large numbers of analytes using large numbers of reagents and processes using multiplexed, independent systems and subsystems for efficient processing and increased throughput of biological analyses.

Abstract: Methods for performing procedures on single analytes at single-analyte resolution are disclosed. The methods utilize an iterative approach to performing a sequence of steps during a single-analyte process. Control of the single-analyte process is achieved by implementing actions during each iteration based upon one or more determined process metrics. Systems are also detailed for implementing the disclosed methods at single-analyte resolution.