Facilitates the application of BLAST+ in the analysis of Next Generation Sequencing (NGS) data. CrocoBLAST runs a pre-calculation to estimate the optimal size of the temporary input files so that maximum speed-up can be achieved on a given machine without negative effect on memory usage. It detects the maximum number of threads for the machine. The tool improves the user experience when working with large data. It is useful for NGS applications that involve annotation as an essential task.