Read length is continuously increasing with the development of novel high-throughput sequencing technologies, which has enormous potentials on cutting-edge genomic studies. However, longer reads could more frequently span the breakpoints of structural variants (SVs) than that of shorter reads. This may greatly influence read alignment, since most state-of-the-art aligners are designed for handling relatively small variants in a co-linear alignment framework. Meanwhile, long read alignment is still not as efficient as that of short reads, which could be also a bottleneck for the upcoming wide application.