Encoding state change of nanopore to reduce data size
A system includes a circuit configured to detect a voltage corresponding to an electrical measurement of a nanopore. The system also includes a component configured to compare the voltage to another voltage. Based at least in part on the comparison, a one bit indicator is determined. The one bit indicator indicates whether the voltage indicates a change in a state of the nanopore. In the event it is determined that the voltage indicates the change in the state of the nanopore, a multiple bit signal is provided for output.
1 . A system, comprising:
a circuit configured to generate a measurement value corresponding to a state of a nanopore; and
a component configured to:
identify, based at least in part on a nanopore state change indicator, whether the measurement value indicates a change in the state of the nanopore,
responsive to determining that the measurement value does not indicate a change in the state of the nanopore, removing the measurement value from output data to reduce a size of the output data; or
responsive to determining that the measurement value indicates a change in the state of the nanopore, compressing the output data based at least in part on characteristics of the output data.
2 . The system of claim 1 , wherein the system is included in a biochip of a nanopore sequencing instrument.
3 . The system of claim 1 , wherein the measurement value is based on a difference in voltage outputs of a pair of analog storage capacitors.
4 . The system of claim 3 , wherein the component is further configured to reset the nanopore state change indicator responsive to determining that the difference is below a threshold.
5 . The system of claim 4 , wherein the measurement value is not included in the output data.
6 . The system of claim 1 , wherein the nanopore state change indicator is a one bit indicator.
7 . The system of claim 1 , wherein the change in the state of the nanopore is a change from an open-channel state to a threaded state.
8 . The system of claim 1 , wherein the change in the state of the nanopore is a change from a first threaded state to a second threaded state or to an open-channel state.
9 . The system of claim 1 , wherein compressing the output data comprises selecting a compression technique from a plurality of compression techniques based on at least one of a profile or a content of the output data.
10 . The system of claim 1 , wherein the plurality of compression techniques include at least one lossy compression technique and at least one lossless compression technique.
11 . The system of claim 1 , wherein the component is further configured to filter the output data responsive to determining that a size of the compressed output data is larger than a threshold.
12 . The system of claim 11 , wherein filtering the output data comprises removing the measurement value from the output data and resetting a status report identifier in a state memory to enable reporting of a subsequent measurement value for the nanopore during a current bright period of a reference AC voltage source signal.
13 . The system of claim 1 , wherein the component is further configured to:
determine an entropy of received data including measurement sample values from a plurality of nanopores; and
select a compression technique based on the entropy.
14 . The system of claim 13 , wherein the selected compression technique is a run-length encoding compression technique responsive to determining the entropy is below a threshold.
15 . The system of claim 13 , wherein the selected compression technique is a Lempel-Ziv-based compression technique responsive to determining the entropy is above a threshold.