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] |