MemAlign: A Memory Structure to Accelerate Gene Sequencing

Since 2003, when the human reference genome was discovered, several applications found gene sequencing a promising mechanism to help improve their results. These include studying hereditary diseases, prenatal monitoring and others. Gene sequencing in its typical configuration consists of several elaborate processing stages, each performed by a separate software package. The intermediate results are transferred via large files between gene sequencing different steps, hence making gene sequencing a processing and I/O demanding task. Taking advantage of advances memory speed and capacity and with the ultimate goal of pipelining the gene sequencing steps and avoiding utilizing file storage to communicate intermediate results, in this paper we present MemAlign, a novel pre-sorted memory structure to pipeline the first and second processing steps of gene sequencing; Alignment and Sort. The number of memory locations of MemAlign corresponds the positions on the human reference genome. Combined with techniques to compress the alignment results, MemAlign essentially eliminates the Sort step by storing alignment results in the memory location that corresponds to the alignment position. MemAlign not only speeds up the combined processing time of Alignment and Sort, but also saves the considerable amount of storage required to store the intermediate results between the two steps.