SortMeRNA is a bioinformatics application designed to filter ribosomal RNA (rRNA) sequences from metatranscriptomic or total RNA sequencing data. It employs a seed-and-extend alignment strategy using a burst trie index for efficient k-mer lookup and Smith-Waterman for alignment extension, coupled with statistical significance testing (E-value) to distinguish rRNA from non-rRNA reads. The tool processes input in parallel via a thread pool and supports both single-end and paired-end reads in FASTA/FASTQ format (including gzipped), producing aligned and non-aligned output files in multiple formats (FASTA, FASTQ, SAM, BLAST-like) along with optional OTU clustering and alignment reports. The application follows a modular architecture with distinct components for input handling (Readfeed), reference indexing (Index/IndexDB), parallel processing (Processor/ThreadPool), alignment computation, and output reporting (various Report* modules). Key features include a checkpoint/resume mechanism implemented using a RocksDB-based key-value store (KVDB) to enable recovery from interruptions, and a portable SIMD layer (SSE2NEON) that allows the same code to leverage vectorized instructions on both x86 and ARM architectures. The build system is managed by CMake with conda-based dependency handling, ensuring reproducibility across platforms. Despite its complexity due to the integration of multiple third-party libraries (zlib, RocksDB, BBHash, Parasail, ALP) and the need for careful version management, the project demonstrates active maintenance with recent commits and a structured release history. The codebase exhibits several well-crafted, reusable components such as the thread pool, KVDB wrapper, and SSE2NEON compatibility layer, which could be extracted for use in other projects with minimal modification. The tool is primarily used in microbiome and transcriptomics workflows for rRNA depletion, a critical preprocessing step in metatranscriptomic analysis.