The paper introduces BWA-SW, a new algorithm for aligning long sequences (up to 1 Mb) against large sequence databases like the human genome. The algorithm is designed to be fast and accurate, outperforming existing methods such as BLAT and SSAHA2 in terms of speed and accuracy. BWA-SW uses a combination of FM-indexes and dynamic programming to efficiently find local matches between the query and reference sequences. The algorithm is particularly effective for long reads, which are becoming more common in sequencing technologies. The authors evaluate BWA-SW on both simulated and real data, demonstrating its superior performance in terms of speed and accuracy compared to other aligners. The paper also discusses the implementation details, heuristics, and comparisons with other methods, highlighting the advantages of BWA-SW in handling long reads and detecting chimera sequences.The paper introduces BWA-SW, a new algorithm for aligning long sequences (up to 1 Mb) against large sequence databases like the human genome. The algorithm is designed to be fast and accurate, outperforming existing methods such as BLAT and SSAHA2 in terms of speed and accuracy. BWA-SW uses a combination of FM-indexes and dynamic programming to efficiently find local matches between the query and reference sequences. The algorithm is particularly effective for long reads, which are becoming more common in sequencing technologies. The authors evaluate BWA-SW on both simulated and real data, demonstrating its superior performance in terms of speed and accuracy compared to other aligners. The paper also discusses the implementation details, heuristics, and comparisons with other methods, highlighting the advantages of BWA-SW in handling long reads and detecting chimera sequences.