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Table 2 Tools for primary processing of metatranscriptomes

From: Experimental design and quantitative analysis of microbial community multiomics

Tool Assembly-based? Requires reference genome? Metatranscriptome-compatible? Automatic statistics and/or figures? Implementation Comments/potential issues Reference
Rockhopper Yes Yes No Yes Java Intended for isolates, not communities [127]
HUMAnN No Yes Yes Yes Python [9]
Tuxedo Yes Yes Yes Yes C++/R [128]
IMP Yes No Yes Yes Python/Docker Relies on binning [129]
SAMSA Pairs only No Yes Yes MG-RAST [130]
COMAN No No Yes Yes Web-based/Python/R Expression distribution of functional groups across phyla [131]
IDBA-MT Yes No No No C++ Only assembles [132]
OASES Yes No No No Only assembles [133]
COGNIZER No No No No C Functional annotation framework for sequences [134]
FMAP No No Yes Yes Perl/R [135]
MEGAN_CE No No Yes Yes Java All taxonomy or function assigned by BLASTing and binning reads [136]
ShotMAP No No Yes Yes Perl/R Several tuning parameters [137]