WHAM (WISCONSIN’S HIGH-THROUGHPUT ALIGNMENT METHOD) is a high-throughput sequence alignment tool developed at University of Wisconsin-Madison. It aligns short DNA sequences (reads) to the whole human genome at a rate of over 1500 million 60bps reads per hour, which is one to two orders of magnitudes faster than the leading state-of-the-art techniques.
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WHAM: A High-throughput Sequence Alignment Method,
Y. Li, A. Terrel and J. M. Patel,
SIGMOD 2011, Athens, Greece