Devices and methods for genome sequencing

A method of genome sequencing, the method comprising:

• storing reference sequences in respective groups of Non-Volatile Memory (NVM) cells of at least one array of NVM cells, each reference sequence representing a portion of a genome;
• loading one or more exact matching phase substring sequences into groups of NVM cells of the at least one array for operation of the at least one array as a Content Addressable Memory (CAM), the one or more exact matching phase substring sequences representing one or more portions of at least one sample read;
• identifying, in an exact matching phase, one or more groups of NVM cells in the at least one array where the stored reference sequence matches the loaded exact matching phase substring sequence, wherein none of the stored reference sequences and the loaded one or more exact matching phase substring sequences include wildcard values when the at least one array operates as a CAM in the exact matching phase;
• loading one or more approximate matching phase substring sequences into groups of NVM cells of the at least one array for operation of the at least one array as a Ternary CAM (TCAM), the one or more approximate matching phase substring sequences representing one or more portions of the at least one sample read;
• identifying, in an approximate matching phase, one or more groups of NVM cells in the at least one array where the stored reference sequence approximately matches the loaded approximate matching phase sequence, wherein at least one of the stored reference sequence and the loaded approximate matching phase substring sequence for each group of NVM cells includes at least one wildcard value when the at least one array operates as a TCAM in the approximate matching phase;
• and
• based on an indication of one or more identified groups of NVM cells from a first array of the at least one array where one or more stored reference sequences match or approximately match a first substring sequence, performing at least one of:
• storing one or more additional reference sequences in a second array of the at least one array;
• and
• loading at least one additional substring sequence into the second array.

A device for genome sequencing, the device comprising:

• at least one array of Non-Volatile Memory (NVM) cells configured to store reference sequences in respective groups of the NVM cells, each reference sequence representing a portion of a genome;
• and
• means for:
• storing the reference sequences in the respective groups of NVM cells of the at least one array;
• loading one or more exact matching phase substring sequences into groups of NVM cells of the at least one array for operation of the at least one array as a Content Addressable Memory (CAM), the one or more exact matching phase substring sequences representing one or more portions of at least one sample read;
• identifying, in an exact matching phase, one or more groups of NVM cells in the at least one array where the stored reference sequence matches the loaded exact matching phase substring sequence, wherein none of the stored reference sequences and the loaded one or more exact matching phase substring sequences include wildcard values when the at least one array operates as a CAM in the exact matching phase;
• loading one or more approximate matching phase substring sequences into groups of NVM cells of the at least one array for operation of the at least one array as a Ternary CAM (TCAM), the one or more approximate matching phase substring sequences representing one or more portions of the at least one sample read;
• and
• identifying, in an approximate matching phase, one or more groups of NVM cells in the at least one array where the stored reference sequence approximately matches the loaded approximate matching phase sequence, wherein at least one of the stored reference sequence and the loaded approximate matching phase substring sequence for each group of NVM cells includes at least one wildcard value when the at least one array operates as a TCAM in the approximate matching phase;
• and
• wherein at least one group of NVM cells in the at least one array is used as part of a CAM in the exact matching phase and is used as part of a TCAM in the approximate matching phase, and wherein the number of NVM cells used to represent a base of an approximate matching phase substring sequence in the at least one group of NVM cells differs from the number of NVM cells used to represent a base of an exact matching phase substring sequence in the at least one group of NVM cells.

A device, comprising:

• a plurality of arrays of Non-Volatile Memory (NVM) cells capable of operating in a Content Addressable Memory (CAM) mode and a Ternary CAM (TCAM) mode;
• and
• circuitry configured to:
• store reference sequences in respective groups of NVM cells of the plurality of arrays;
• load one or more exact matching phase substring sequences into groups of NVM cells of the plurality of arrays;
• set the plurality of arrays in the CAM mode and identify, in an exact matching phase, one or more groups of NVM cells where the stored reference sequence matches the loaded exact matching phase substring sequence;
• load one or more approximate matching phase substring sequences into groups of NVM cells of the plurality of arrays;
• and
• set the plurality of arrays in the TCAM mode and identify, in an approximate matching phase, one or more groups of NVM cells where the stored reference sequence approximately matches the loaded approximate matching phase substring sequence, wherein at least one of the compared reference sequence and the approximate matching phase substring sequence includes at least one wildcard value in the approximate matching phase;
• and
• wherein at least one group of NVM cells in the plurality of arrays is used as a CAM in the exact matching phase and is used as a TCAM in the approximate matching phase, and wherein the number of NVM cells used to represent a base of an approximate matching phase substring sequence in the at least one group of NVM cells differs from the number of NVM cells used to represent a base of an exact matching phase substring sequence in the at least one group of NVM cells.