Bioinformatics Systems, Apparatuses, and Methods Executed on an Integrated Circuit Processing Platform

Abstract

A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes a structured ASIC formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the structured ASIC connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

What is claimed is: 
     
         1 . An apparatus for executing one or more steps of a sequence analysis pipeline on genetic sequence data of a subject, the genetic sequence data comprising one or more of a read of genomic data, one or more genetic reference sequences, and an index of the genetic reference sequence, the apparatus comprising:
 an integrated circuit comprising a set of reconfigurable hardwired digital logic circuits that are interconnected by a plurality of physical electrical interconnects, one or more of the plurality of physical electrical interconnects comprising an input for receiving one or more of the read of genomic data and the one or more genetic reference sequences, the set of reconfigurable hardwired digital logic circuits being in a wired configuration to receive location information specifying a reference segment of the one or more genetic reference sequences, to access the one or more genetic reference sequences based on the location information, and to align the read of genomic data to the one or more segments of the one or more genetic reference sequences, the aligning comprising:
 generating a linear array of a plurality of scoring cells to calculate alignment scores within a band of a two-dimensional alignment matrix, the two-dimensional alignment matrix having a first dimension representing a query segment from the read, and a second dimension representing the reference segment of the one or more genetic reference sequences;
 each scoring cell having one or more score outputs to transmit scores to an associated one or two neighboring cells, one or more score inputs to receive scores from the one or two neighboring cells, a query base input to receive a query base, and a reference base input to receive a reference base, and being configured to compute a new score within the band at a position in the two-dimensional alignment matrix corresponding to the received query base and the received reference base, 
 the new score being computed using the received scores from the one or two neighboring cells and using a match score based on a comparison of the received query base and the received reference base; 
 wherein positions of the new scores computed by the scoring cells of the linear array represent a wavefront traversing the two-dimensional alignment matrix; and 
 further wherein the query bases are shifted sequentially from the query sequence through the linear array in a first direction, each shift of the query bases corresponding to a step of the wavefront along the first dimension of the alignment matrix, and the reference bases are shifted sequentially from the reference segment through the linear array in a second direction opposite the first direction, each shift of the reference bases corresponding a step of the wavefront along the second dimension of the alignment matrix.