Parallel architecture and hardware implementation of pre-processor and post-processor for sequence assembly

In current DNA sequence assembly flows, a time-consuming pre-processing routine is usually executed to remove low quality data for smaller problem sizes and better final results. The step usually takes 25%~90% of the total computation time. To speed up the process, based on the characteristics of DNA data, we propose to use digital processing hardware, with parallel and pipeline capabilities, to accelerate the pre-processing step. In our FPGA implementation, the computing speed can be improved up to 2,700 folds. With similar design concepts, we also implement a post-processor to convert assembly results from color space to base space whenever the step is necessary. Both designs enable faster sequence assembly, which will greatly benefit the research in genomics and related fields.