Next-generation sequencing (NGS) appears to be very promising to study miRNAs comprehensively, which can not only profile known miRNAs, but also predict novel miRNAs. There are an increasing number of software tools developed for microRNA NGS
data analysis. Nevertheless, an overall comparison of these tools is still rare and how divergent these software tools are is still unknown, which confuses the researchers to select an optimal tool. In our study, we performed a comprehensive comparison of seven representative software tools based on real data in various aspects, including detected known miRNAs, miRNAs abundance, differential expression and predicted novel miRNAs.
We presented the divergences and similarities of these tools and gave some basic evaluation of the tools’ performances. In addition, some extreme cases in miRNAkey were explored. The comparison of these tools suggests that the performances of these software
tools are very diverse and the caution is necessary to take when choosing a software tool. The summarization of the tools’ features and comparison of their performances in our study will provide useful information for the researchers to promote their selection of an appropriate software tool.