Table 3.

Brief description of metatranscriptomics tools: advantages and disadvantages.

Tool	Bioinformatics tools for metatranscriptomics
	Brief description	Advantages	Disadvantages
HUMAnN2	Pipeline for profiling the presence/absence and activity level of microbial pathways in a community.	Easy to install and extensive documentation and examples. Uses commonly available tools and databases.	Command line interface.
MetaTrans	Pipeline aiming to analyze structure and functions of active microbial communities using the power of multi-threading computers.	Its design facilitates the inclusion of third-party tools in each of its stages. Possibility to perform RNA-Seq analyses addressing both 16S rRNA taxonomy and gene expression.	Installation on local computer may be difficult for non-experts. Require proper local setup on a powerful computer.
COMAN	Web-based tool dedicated to automatically and comprehensively analyzing metatranscriptomic data.	Easy-to-use interface and extensive instructions for non-experts. Processes uploaded raw reads automatically to ultimately achieve functional assignments, which are then exploited to perform further analysis.	Web-based interface not suitable for big analysis.