mm2-plus: Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)

mm2-plus is an fast long-read to genome and genome-to-genome aligner, built on top of minimap2 (Minimap2-2.28 (r1209)). We incorporated optimizations from mm2-fast (v1.0) and implemented parallel algorithms for efficient genome-to-genome alignment. The optimizations include: Parallel chaining Faster interval tree-based algorithm for selecting primary chains AVX2/AVX512 SIMD alignment (from mm2-fast) AVX2/AVX512 SIMD chaining (from Intel TAL) Parallel sorting (GNU parallel stable sort std::stable_sort) mm2-plus serves as a drop-in replacement for minimap2, providing near-identical output while significantly reducing execution time, especially for genome-to-genome alignments.