Memory-safe high-performance sequence mapping with rammap

Abstract

We introduce a reimplementation of the widely used mapping tool minimap2 in Rust called rammap. We demonstrate perfect concordance with minimap2, enabling its backwards compatibility as a drop-in replacement for minimap2-based workflows. Additionally, rammap implements performance optimizations for modern architectures and applications, including AVX512 and WASM v128 SIMD support for dynamic programming alignment and SIMD-accelerated chaining. These achieve comparable or better performance than minimap2 across diverse mapping workloads while maintaining Rusts stronger memory safety constraints. The rammap API exposes both SIMD-accelerated sequence-sequence alignment modules and full mapping pipelines for use as an integrated library. Lastly, we describe the modular architecture and provide examples illustrating the extensibility of major mapping components, including seeding, chaining, and gap-filling/extension to support development of improved or domain-specific mapping components within a high-performance framework.