公开(公告)号：US20180239864A1

公开(公告)日：2018-08-23

申请号：US15554592

申请日：2016-02-17

Applicant: INDIAN INSTITUTE OF SCIENCE

Inventor： Santhi NATARAJAN ,  Debnath PAL ,  S. K. NANDY

IPC: G06F19/22 ,  G06F19/28

CPC classification number: G16B30/00 ,  G16B50/00

Abstract: The present disclosure relates to an aligner in a hardware accelerator that can align short reads with a reference genome as genomic data is streamed through the hardware accelerator and thus can speed up the process of alignment. In an aspect, the disclosed short read aligner can incorporate a number of hardware kernels modelled as processor array implementation of the cost function model of the dynamic programming algorithm having a number of processing elements, wherein each kernel can incorporate a traceback control block as a separate hardware that enables traceback in parallel to the processor array and alignment matrix filling process by use of trace back direction vectors and using additional trackback path prediction features. The disclosed aligner can be parameterized and can perform alignment for cost function models of different variations of chosen dynamic programming algorithm. The aligner incorporates adequate sequence partitioning, scheduling, alignment and stitching schemes to accommodate short reads of variable lengths for alignment.