Both academic and enterprise software solutions exist for designing CRISPR targets. They offer advantages when designing guide RNAs (gRNAs) but often focus on a select number of model organisms. Those that offer a wide variety of organisms can be limited in support of alternative endonucleases and downstream analyses such as multitargeting and population analyses to interrogate a microbiome. To accommodate broad CRISPR utilization, we developed a flexible platform software CRISPR Associated Software for Pathway Engineering and Research (CASPER) for gRNA generation and analysis in any organism and with any CRISPR-Cas system. CASPER combines traditional gRNA design tools with unique functions such as multiple Cas-type gRNA generation and evaluation of spacer redundancy in a single species or microbiome. The analyses have implications for strain-, species-, or genus-specific CRISPR diagnostic probe design and microbiome manipulation. The novel features of CASPER are packaged in a user-friendly interface to create a computational environment for researchers to streamline the utility of CRISPR-Cas systems.