An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of non-human sequences in deep sequencing datasets. RINS is optimized for mate-paired high-throughput sequencing data with reads at least 36 bp and up to 500 bp, and can be run on sequencing data from any species. Non-paired end sequencing data can also be used, though contig generation and extension will be less robust. In <2 h, RINS correctly identified the known virus in the dataset SRR73726 and is compatible with any computer capable of running the prerequisite alignment and assembly programs. RINS accurately identifies sequencing reads from intact or mutated non-human genomes in a dataset and robustly generates contigs with these non-human sequences.