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Next-generation sequencing (NGS) has been widely applied to biological and medical researches for its efficient production of DNA short reads nowadays. Among various applications, de novo sequence assembly is a technique using NGS short reads to obtain a whole genome with no reference. To make assembly results accurate, it is a common practice to filter out low-quality data at the early stage of the...
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...
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