Metagenomics has revolutionized the study of microbial communities by facilitating direct genetic analysis of environmental samples. This article proposes a novel metagenomic pipeline that integrates alignment-free k-mer screening using Mash Screen with precise approximate mapping via MashMap. The pipeline dynamically constructs targeted reference databases, reducing computational overhead while enhancing representativeness. Taxonomic assignments are strengthened by a weighted strategy based on alignment coverage and confidence scoring. Results demonstrate excellent F1 scores, particularly for prokaryotes and viruses, with scores exceeding 0.95 across all taxonomic levels. The pipeline processes most datasets in under 60 min with a memory footprint of approximately 5.82 GB, making it suitable for high-throughput analyses. By addressing the limitations of existing tools, this pipeline offers a scalable, accurate and user-friendly solution for the analysis of microbial communities, advancing our understanding of complex ecosystems and their functional potential.