SYSTEMS AND METHODS FOR FLOW CELL SAMPLE ALLOCATION

1 . A method implemented on one or more computers having one or more processors for pooling a plurality of biological specimens for short read next generation sequencing, each specimen included in the plurality of specimens associated with a first plurality of specimen characteristics and a second plurality of specimen characteristics, the method comprising:

identifying a plurality of flow cell characteristics for each flow cell included in a plurality of flow cells;

selecting, by the one or more processors, one or more of the flow cells in the plurality of flow cells based at least in part on the plurality of flow cell characteristics and the first plurality of specimen characteristics, wherein the first plurality of specimen characteristics includes a mass of each specimen and at least one other specimen characteristic;

selecting, by the one or more processors, which specimens to put in each lane of each selected one or more of the flow cells based at least in part on the second plurality of specimen characteristics and at least one lane characteristic;

generating, by the one or more processors and for each lane including one or more specimens, at least one pool of specimens based at least in part on a placement of the selected specimens into respective lanes of the selected one or more of the flow cells; and

outputting, by the one or more processors, the generated pools.

2 . (canceled)

3 . The method of claim 1 , wherein the outputting the generated pools comprises:

outputting the generated pools to a flow cell allocation system.

4 . The method of claim 1 , wherein the outputting the generated pools comprises:

outputting the generated pools to a display for viewing by a lab technician.

5 . (canceled)

6 . The method of claim 1 further comprising:

sequencing the at least one specimen in each outputted pool to generate sequencing information.

7 . The method of claim 1 , wherein a flow cell characteristic in the plurality of flow cell characteristics is an availability of a flow cell in the plurality of flow cells, wherein when a flow cell is unavailable, the method further comprises:

delaying sequencing the unavailable flow cell until the unavailable flow cell becomes available.

8 . The method of claim 1 , wherein the plurality of specimens comprises blood sample specimens, and the at least one pool in a selected lane comprises at least a portion of the blood specimens.

9 . The method of claim 1 , wherein the plurality of specimens comprises liquid sample specimens, and the at least one pool in a selected lane comprises at least a portion of the liquid specimens.

10 . The method of claim 9 , wherein the selected lane including the pool comprising at least a portion of the liquid specimens has a second pool comprising solid samples.

11 . The method of claim 1 , wherein the outputting the generated pools comprises:

outputting the generated pools to a whole genome processing system.

12 . (canceled)

13 . (canceled)

14 . The method of claim 1 , wherein

the step of selecting one or more of the flow cells includes evaluating a number of specimens included in the plurality of specimens in addition to evaluating the plurality of flow cell characteristics and the first plurality of specimen characteristics,

and wherein the step of selecting which specimen to put in each lane of each selected one or more of the flow cells includes:

determining a first plurality of flow cell specimen configurations based on the second plurality of specimen characteristics and the at least one lane characteristic, each of the first plurality of flow cell specimen configurations configured to house each specimen included in the plurality of specimens; and

determining a second plurality of flow cell specimen configurations based on the second plurality of specimen characteristics, the at least one lane characteristic, and at least one constraint, each flow cell specimen configuration included in the second plurality of flow cell specimen configurations comprising a flow cell specimen configuration included in the first plurality of flow cell specimen configurations.

15 . The method of claim 14 , wherein the plurality of flow cell characteristics comprises a turnaround time, the step of selecting which specimens to put in each lane of each selected one or more of the flow cells comprises:

generating, a plurality of hold costs based on the turnaround time associated with each specimen included in the plurality of specimens, each specimen included in the plurality of specimens being associated with a hold cost included in the plurality of hold costs, and the second plurality of flow cell specimen configurations being determined based on the plurality of hold costs; and

allocating specimens included in a specific flow cell specimen configuration included in the second plurality of flow cell specimen configurations to the at least one flow cell associated with the specific flow cell specimen configuration.

16 . The method of claim 14 , wherein the first plurality of specimen characteristics further comprise a unique identifier, a source tissue type, an age, and a turn-around-time.

17 . The method of claim 14 , wherein the plurality of flow cell characteristics comprises a maximum capacity, a minimum capacity, and a number of lanes, the first plurality of specimen characteristics comprises a barcode, and the step of selecting one or more of the flow cells comprises:

generating a preliminary set of flow cell groups comprising unique combinations of one or more flow cells included in the plurality of flow cells;

determining a secondary set of flow cell groups based on a number of specimens included in the plurality of specimens comprising at least a portion of the preliminary set of flow cell groups by, for each flow cell group included in the secondary set of flow cell groups:

determining that the maximum capacity of each flow cell included in the flow cell group is not exceeded by the number of specimens; and

determining that the minimum capacity of each flow cell included in the flow cell group is satisfied by the number of specimens;

determining a maximum number of repeated barcodes based on the barcode associated with each specimen in the plurality of specimens; and

determining a tertiary set of flow cell groups by determining, for each flow cell group included in the secondary set of flow cell groups, that a sum of the number of lanes associated with each flow cell in the flow cell group is at least as great as the maximum number of repeated barcodes, the set of flow cell groups comprising the tertiary set of flow cell groups.

18 . The method of claim 14 , wherein the plurality of flow cell characteristics comprises a maximum capacity, a minimum capacity, and a number of lanes, the second plurality of specimen characteristics comprises a barcode, and the determining the first plurality of flow cell specimen configurations comprises:

determining, for a specific flow cell specimen configuration included in the first plurality of flow cell specimen configurations, that the maximum capacity and the minimum capacity of each flow cell included in the specific flow cell specimen configuration can be satisfied while keeping specimens associated with equal barcodes in different lanes included in the specific flow cell specimen configuration based on the number of lanes associated with each flow cell in the target flow cell specimen configuration and the barcode associated with each specimen included in the plurality of specimens.

19 . The method of claim 14 , wherein the second plurality of specimen characteristics comprises the specimen type, wherein the specimen type is selected from a tumor, a normal match, and a control, and the determining the first plurality of flow cell specimen configurations comprises:

determining, for each flow cell specimen configuration included in the first plurality of flow cell specimen configurations, a processing cost based on the specimen type associated with the flow cell specimen configuration and the flow cell data; and

ranking each flow cell specimen configuration included in the first plurality of flow cell specimen configurations based on the processing cost associated with the flow cell specimen configuration.

20 . The method of claim 14 , wherein the plurality of flow cell characteristics comprises a turnaround time and the determining the second plurality of flow cell specimen configurations comprises:

generating, from the second plurality of flow cell specimens, unique pairs of specimens;

generating a plurality of compatibility scores based on the specimen data, each unique pair of specimens being associated with a compatibility score included in the plurality of compatibility scores;

generating a plurality of hold costs based on the turnaround time associated with each specimen included in the plurality of specimens, each hold cost included in the plurality of hold costs being associated with a specimen included in the plurality of specimens; and

wherein the step of generating at least one pool of specimens comprises generating a plurality of pools based on the plurality of compatibility scores and the plurality of hold costs, each pool included in the plurality of pools comprising at least one specimen.

21 . The method of claim 20 , wherein the step of selecting one or more of the flow cells further comprises:

generating a plurality of preliminary flow cell specimen configurations based on at least a portion of the plurality of pools and the at least one constraint, the second plurality of flow cell specimen configurations comprising at least a portion of the plurality of preliminary flow cell specimen configurations.

22 . The method of claim 14 , wherein the step of generating at least one pool of specimens comprises:

generating a first set of pools based on the second plurality of specimen characteristics, the at least one lane characteristic, and a first constraint included in the at least one constraint, each pool included in the first set of pools comprising at least one specimen included in the plurality of specimens; and

generating a second set of pools comprising a subset of the first set of pools based on the second plurality of specimen characteristics, the at least one lane characteristic, and a second constraint included in the at least one constraint.

23 . The method of claim 22 , wherein the step of generating at least one pool of specimens further comprises:

determining a group of one or more pools included in the second set of pools that satisfies the second constraint, and wherein the allocating the at least a portion of the specimens included in the plurality of specimens to one or more flow cells included in the plurality of flow cells comprises:

placing each pool included in the group of one or more pools into one or more lanes included in the one or more flow cells.

24 . The method of claim 14 , wherein the at least one constraint comprises at least one of a maximum pool mass, a maximum lane mass, a maximum flow cell mass, a minimum pool mass, a minimum lane mass, a minimum flow cell mass, a mass balancing threshold, a turnaround time constraint, a prioritization level, or a flow cell cost.

25 . The method of claim 14 , wherein the at least one constraint comprises a hard constraint.

26 . The method of claim 14 , wherein the at least one constraint comprises a soft constraint.

27 . A biological specimen pooling system for pooling a plurality of biological specimens for short read next generation sequencing, each specimen included in the plurality of specimens associated with a first plurality of specimen characteristics and a second plurality of specimen characteristics, the system comprising at least one processor and at least one memory comprising instructions to:

identify a plurality of flow cell characteristics for each flow cell included in a plurality of flow cells;

select, by the one or more processors, one or more of the flow cells in the plurality of flow cells based at least in part on the plurality of flow cell characteristics and the first plurality of specimen characteristics, wherein the first plurality of specimen characteristics includes a mass of each specimen and at least one other specimen characteristic;

select, by the one or more processors, which specimens to put in each lane of each selected one or more of the flow cells based at least in part on the second plurality of specimen characteristics and at least one lane characteristic;

generate, by the one or more processors and for each lane including one or more specimens, at least one pool of specimens based at least in part on a placement of the selected specimens into respective lanes of the selected one or more of the flow cells; and

output, by the one or more processors, the generated pools.

28 . The system of claim 27 , wherein the memory further comprises instructions to:

as part of the step of selecting one or more of the flow cells, evaluate a number of specimens included in plurality of specimens in addition to evaluating the plurality of flow cell characteristics and the first plurality of specimen characteristics,

and, as part of the step of selecting which specimens to put in each lane of each selected one or more of the flow cells, determine a first plurality of flow cell specimen configurations based on the second plurality of specimen characteristics and the at least one lane characteristic, each of the first plurality of flow cell specimen configurations configured to house each specimen included in the plurality of specimens; and

determine a second plurality of flow cell specimen configurations based on the second plurality of specimen characteristics, the at least one lane characteristic, and at least one constraint, each flow cell specimen configuration included in the second plurality of flow cell specimen configurations comprising a flow cell specimen configuration included in the first plurality of flow cell specimen configurations.

29 . The system of claim 27 , wherein the memory further comprises instructions to:

output the at least one pool to a flow cell allocation system.

30 . A non-transitory computer-readable storage medium having stored thereon program code instructions that, when executed by a processor, cause the processor to perform a method for pooling a plurality of biological specimens for short read next generation sequencing, each specimen included in the plurality of specimens associated with a first plurality of specimen characteristics and a second plurality of specimen characteristics, the method comprising:

identifying a plurality of flow cell characteristics for each flow cell included in a plurality of flow cells;

selecting, by the one or more processors, one or more flow cells in the plurality of flow cells based at least in part on the plurality of flow cell characteristics and the first plurality of specimen characteristics, wherein the first plurality of specimen characteristics includes a mass of each specimen and at least one other specimen characteristic;

selecting, by the one or more processors, which specimens to put in each lane of each selected one or more of the flow cells based at least in part on the second plurality of specimen characteristics and at least one lane characteristic;

generating, by the one or more processors and for each lane including one or more specimens, at least one pool of specimens based at least in part on a placement of the selected specimens into respective lanes of the selected one or more of the flow cells; and

outputting, by the one or more processors, the generated pools.

31 . The method of claim 3 , further comprising:

arranging, by the flow cell allocation system, the plurality of specimens in associated pools.

32 . The method of claim 4 , further comprising:

arranging, by the lab technician, the plurality of specimens in associated pools.