MEMOCODE 2012 hardware/software codesign contest: DNA sequence aligner

The MEMOCODE design contest for 2012 is exact substring matching: a simplified form of the DNA sequence alignment problem. The challenge is to efficiently locate millions of 100-base-pair short read sequences in a 3-million-base-pair reference genome. Contestants had a month to create a fast system that ran on a given set of test data. Entries were judged both on absolute time and the product of time and system cost. The two winning groups, which were invited to contribute papers describing their solutions, judiciously chose algorithms that exploited powerful hardware. The two winning entries employed a hash algorithm running on a Convey HC-1 FPGA/multicore hybrid with an aggressive memory system and a Burrows-Wheeler/hash hybrid running on a 12-core Intel system was second.