Aim. RNA sequencing (RNA–seq) has become an exemplary technology in biology and clinical applications, outperforming other transcriptomic profiling protocols due to its precision and accuracy in characterising transcriptomes. As RNA–seq analysis gains popularity and becomes an essential component of future precision medicine, examining the software development and open science practices used by RNA–seq tools is necessary to ensure and improve the accuracy of generated results. Conclusions. In addition to software development practices, it is vital to follow best practices in benchmarking and validation of developed tools. Ideally, a newly developed tool would be compared against all previously developed tools, but it is currently unknown if this practice is widely adopted in the bioinformatics community. Examining these studies is vital to develop RNA–seq tools that can not only enhance the precision and thoroughness of all future benchmarking studies, but also encourage tool developers to engage in more comprehensive benchmarking when releasing their tools. By highlighting promising trends in usability, accessibility, maintainability, and benchmarking practices, we aim to encourage wider adoption of these best practices within the biomedical research community. This collective effort will ultimately lead to the development of more accurate, robust, and user–friendly RNA–seq tools in the future.