SOAP3 is a GPU-based software for aligning short reads with a reference sequence.It can find all alignments with k mismatches, where k is chosen from 0 to 3 (see Section 3.2 for other options including finding only the best alignments and trimming the reads). When compared with its previous version SOAP2, SOAP3 can be up to tens of times faster. For example, when aligning length-100 reads with the human genome, SOAP3 is the first software that can find all 3-mismatch alignments in tens of seconds per one million reads. The alignment program in this package is optimized to work for multi-millions of short reads each time by running a multi-core CPU and the GPU concurrently. To exploit the parallelism of the GPU effectively, SOAP3 is using an adapted version of the 2BWT index of SOAP2 (the new index is called the GPU-2BWT). The index and algorithms were developed by the algorithms research group of the University of Hong Kong (T.W. Lam, C.M. Liu, Thomas Wong, Edward Wu and S.M. Yiu).