UNLABELLED: The growing number of metagenomic studies in medicine and environmental sciences is creating increasing demands on the computational infrastructure designed to analyze these very large datasets. Often, the construction of ultra-fast and precise taxonomic classifiers can compromise on their sensitivity (i.e. the number of reads correctly classified). Here we introduce CLARK-S, a new software tool that can classify short reads with high precision, high sensitivity and high speed. AVAILABILITY AND IMPLEMENTATION: CLARK-S is freely available at http://clark.cs.ucr.edu/ CONTACT: stelo@cs.ucr.eduSupplementary information: Supplementary data are available at Bioinformatics online.