Table 1.

A list of metatranscriptomics pipelines and their capabilities.

		Read based					Assembly based
		MetaTrans	COMAN	FMAP	SAMSA2	HUMAnN2	SqueezeMeta	IMP	MOSCA
Preprocessing	QC	✓	✓	✓	✓	×	✓	✓	✓
	Removes host reads	×	×	✓	×	×	×	✓	×
	Removes rRNA	✓	✓	×	✓	×	✓	✓	✓
de novo Assembly		×	×	×	×	×	✓	✓	✓
Binning		×	×	×	×	×	✓	✓	×
Taxonomic Profiling	Reads	✓	✓	×	✓	✓	×	×	×
	Contigs	×	×	×	×	×	✓	✓	✓
Functional Annotation	Reads	✓	✓	✓	✓	✓	×	×	×
	Contigs	×	×	×	×	×	✓	✓	✓
Pathway Analysis		✓	✓	✓	×	✓	✓	✓	×
Requires Metagenomes		×	×	×	×	×	×	✓	×
Summary Report		×	×	×	×	×	×	✓	×
Web Interface		×	✓	×	×	×	×	×	×
Multiple Sample Comparisons		✓	✓	✓	✓	✓	✓	×	✓
Differential Expression		✓	✓	✓	✓	×	×	×	✓
Docker		×	×	×	×	✓	×	✓	✓
Conda		×	×	×	×	✓	×	✓	×
Long Read Support		×	×	×	×	×	✓	×	×
Public Code Repository		✓	×	✓	✓	✓	✓	✓	✓