Table 3.
Summary of available software pipelines for taxonomic and/or functional analysis of metagenomic data
| Tools | Sequence processing | Taxonomic profiling | Functional profiling | Annotation level | Ref. |
|---|---|---|---|---|---|
| MetaCRAM | Mapping (Bowtie2) | Kraken | Taxon, gene | (5) | |
| SUPER-FOCUS | Mapping (RAPSearch2) | FOCUS | GenBank database | Taxon, gene | (47) |
| MOCAT2 | Assembly (SOAPdenovo) and gene prediction (MetaGeneMark) | eggNOG database | eggNOG database and others | Taxon, gene | (4) |
| MetaStorm | Assembly (IDBA-UD) and gene prediction (PRODIGAL) | SILVA and GREENGENES databases | CARD and CAZy databases | Taxon | (48) |
| CAMAMED | Mapping (MOSAIK) | MetaPhlAn2 | KAAS and GhostKOALA web services and KEGG database | Taxon, gene, KO, EC number and reaction | Present work |