VirSieve Pipeline is a bioinformatic pipeline designed for the detection and identification of viral mutant sequences from difficult matrices such as wastewater. This pipeline is currently optimized for SARS-CoV-2, but can be adapted to many other viral species. VirSieve automates the process of alignment, primer trimming (if needed), variant calling, and variant annotation. VirSieve has an emphasis on identifying which mutations are more likely to be biologically present and which can be explained by sequencing or analysis artifacts or are otherwise potentially spurious. VirSieve is built around software containers and comes with pre-build reference data to ensure consistency between runs and between different labs.