Flow cell with integrated manifold

A method comprising:

• connecting a flow cell to an instrument, the flow cell comprising a plurality of inlet ports, an outlet port and a flow channel in fluid communication therebetween, the flow channel comprising a manifold section having a manifold section swept volume and a detection section having a detection section swept volume, wherein a ratio of the detection section swept volume to manifold section swept volume is at least about 10 to 1;
• operating a first valve of a plurality of valves of the instrument to select a first reagent of a plurality of reagents, each reagent positioned in a reagent well of one of a cartridge or the instrument;
• pumping the first reagent through a first inlet port of the plurality of inlet ports and through the flow channel of the flow cell;
• performing a first chemical reaction between the first reagent and analytes positioned in the detection section of the flow channel, wherein at least some of the first reagent remains in the flow channel as a remaining reagent after completion of the first chemical reaction;
• operating a subsequent valve of the plurality of valves to select a subsequent reagent of the plurality of reagents;
• and
• pumping the subsequent reagent through a subsequent inlet port of the plurality of inlet ports and through the flow channel to flush out the remaining reagent from the flow channel, wherein, due at least in part to the ratio of the detection section swept volume to the manifold section swept volume being at least about 10 to 1, a concentration of at least about 99.95 percent of reagent positioned in the detection section is the subsequent reagent, after pumping a total volume of the subsequent reagent through the flow channel that is equal to or less than about 2.5 times a total swept volume of the manifold section plus the detection section.