公开(公告)号：US20200265923A1

公开(公告)日：2020-08-20

申请号：US16749139

申请日：2020-01-22

Applicant: THE REGENTS OF THE UNIVERSITY OF MICHIGAN

Inventor： Arun SUBRAMANIYAN ,  Satish NARAYANASAMY ,  Reetuparna DAS ,  David T. BLAAUW

IPC: G16B30/10 ,  G06F16/22

Abstract: Read alignment is a time-consuming step in genome sequencing analysis. The most widely used software for read alignment, BWA-MEM and BWA-MEM2 are based on the seed-and-extend paradigm for read alignment. The seeding step of read alignment is a major bottleneck contributing ˜38% of the overall execution time in BWA-MEM2 when aligning whole human genome. This is because BWA-MEM2 uses a compressed index structure called the FMD-Index, which results in high bandwidth requirements, primarily due to its character-by-character processing of reads. To address these challenges, a novel seeding data structure is presented along with a custom accelerator architecture for seeding.

公开(公告)号：US20200285479A1

公开(公告)日：2020-09-10

申请号：US16296507

申请日：2019-03-08

Applicant: Arm Limited ,  The Regents of The University of Michigan

Inventor： Vaibhav GOGTE ,  Wei WANG ,  Stephan DIESTELHORST ,  Peter M. CHEN ,  Satish NARAYANASAMY ,  Thomas Friedrich WENISCH

IPC: G06F9/38 ,  G06F9/52

Abstract: A data processing apparatus includes obtain circuitry that obtains a stream of instructions. The stream of instructions includes a barrier creation instruction and a barrier inhibition instruction. Track circuitry orders sending each instruction in the stream of instructions to processing circuitry based on one or more dependencies. The track circuitry is responsive to the barrier creation instruction to cause the one or more dependencies to include one or more barrier dependencies in which pre-barrier instructions, occurring before the barrier creation instruction in the stream, are sent before post-barrier instructions, occurring after the barrier creation instruction in the stream, are sent. The track circuitry is also responsive to the barrier inhibition instruction to relax the barrier dependencies to permit post-inhibition instructions, occurring after the barrier inhibition instruction in the stream, to be sent before the pre-barrier instructions.

公开(公告)号：US20200234795A1

公开(公告)日：2020-07-23

申请号：US16749039

申请日：2020-01-22

Applicant: THE REGENTS OF THE UNIVERSITY OF MICHIGAN

Inventor： Xiao WU ,  Satish NARAYANASAMY ,  Reetuparna DAS ,  David T. BLAAUW

IPC: G16B30/10 ,  G16B20/20

Abstract: A method is presented for aligning a read with a haplotype. The method includes: constructing an overall matrix for computing alignment probabilities between a given read and a given haplotype, calculating, during a first pass, an alignment probability for each cell in the overall matrix using Pair-HMM method, where the alignment probabilities are calculated using fixed-point arithmetic; pruning cells from the overall matrix to derive a subset of unpruned cells; and calculating, during a second pass, an alignment probability for each cell in the subset of unpruned cells using the Pair-HMM method, where the alignment probabilities are calculated using floating-point arithmetic.

公开(公告)号：US20200234796A1

公开(公告)日：2020-07-23

申请号：US16749679

申请日：2020-01-22

Applicant: THE REGENTS OF THE UNIVERSITY OF MICHIGAN

Inventor： Satish NARAYANASAMY ,  Daichi FUJIKI ,  David T. BLAAUW ,  Reetuparna DAS ,  Shunhao WU

IPC: G16B30/10

Abstract: A method is presented for aligning a read with a reference substring of a genome sequence. The method includes: receiving a banded portion of a matrix from a sequence alignment algorithm; calculating a score threshold for the banded portion of the matrix, where value of the score threshold is calculated as a function of a scoring method used by the sequence alignment algorithm; identifying a high score amongst the cells in the banded portion of the matrix; and comparing the high score to the score threshold. Performing variant calling using the banded portion of the matrix when the high score is greater than to the score threshold. Computing alignment scores for a larger portion of the matrix using the sequence alignment algorithm when the high score is less than or equal to the score threshold.

公开(公告)号：US20180300261A1

公开(公告)日：2018-10-18

申请号：US15485860

申请日：2017-04-12

Applicant: THE REGENTS OF THE UNIVERSITY OF MICHIGAN

Inventor： Satish NARAYANASAMY ,  Shaizeen AGA

IPC: G06F12/14 ,  G06F21/60 ,  G06F21/72 ,  G06F13/16 ,  G06F13/40 ,  G06F13/42

Abstract: A system that executes private enclave functions in a secure high-performance host processor connected to an enhanced memory unit through a conventional memory bus using a packetized interface is disclosed. The logic layer of the enhanced memory unit is included in a trusted computing base (TCB) and is used to implement cryptographic functions. Storage layers of the enhanced memory unit remain outside the TCB and are used to store encrypted data and associated meta-data.