Table 1.
Tools grouped according to their main functionality.
| Shotgun metagenomics | Assembly | EULER41 |
| Velvet42 | ||
| SOAP43 | ||
| ABySS44 | ||
| MetaVelvet46 | ||
| MetaVelvet-SL45 | ||
| Meta-IDBA47 | ||
| IDBA-UD48 | ||
| Newbler (Roche) | ||
| MIRA37 | ||
| Mapsembler171 | ||
| ALLPATHS172,173 | ||
| MetaORFA174,175 | ||
| MetAMOS38 | ||
| Binning | TETRA51 | |
| S-GSOM52 | ||
| PhylopythiaS54,55 | ||
| TACOA56 | ||
| PCAHIER57 | ||
| ESOM58 | ||
| ClaMS60 | ||
| CARMA61 | ||
| WGSQuikr176 | ||
| SPHINX177 | ||
| MetaPhyler62 | ||
| SOrt-ITEMS63 | ||
| PhymmBL70 | ||
| MetaCluster71,72 | ||
| Annotation | FASTX-Toolkit74 | |
| FastQC67 | ||
| SolexaQA78 | ||
| Lucy 279 | ||
| DUST82 | ||
| Bowtie83 | ||
| MetaGeneMark84 | ||
| LEfSe19 | ||
| TACOA56 | ||
| Metagene85 | ||
| CREST178 | ||
| Prodigal86 | ||
| mOTU-LG179 | ||
| Orphelia87 | ||
| Kraken180 | ||
| FragGeneScan88 | ||
| CRT89 | ||
| NBC181 | ||
| MyTaxa182 | ||
| RITA183 | ||
| PILER-CR90 | ||
| tRNAscan184 | ||
| KEGG99 | ||
| MetaCluster TA71 | ||
| SEED100 | ||
| eggNOG101 | ||
| ProViDE185 | ||
| COG/KOG186 | ||
| PFAM103,104,187 | ||
| TIGRFAM105 | ||
| MetaPhlAn188 | ||
| HighSSR189 | ||
| Blat107 | ||
| Analysis pipelines | IMG/MER64,190 | |
| MG-RAST65 | ||
| MEGAN 567–69 | ||
| CAMERA112 | ||
| Parallel-META74,191 | ||
| EBI Metagenomics108 | ||
| METAREP192 | ||
| PHACCS193 | ||
| Marker gene metagenomics | Standalone software | QIIME111,194 |
| Mothur121 | ||
| JAguc195 | ||
| M-pick196 | ||
| OTUbase197 | ||
| CopyRighter198 | ||
| AbundantOTU199 | ||
| UniFrac145,200 | ||
| ESPRIT141,201 | ||
| Analysis pipelines | SILVA125 | |
| FunFrame202 | ||
| PANGEA203 | ||
| FastGroupII204 | ||
| CLOTU205 | ||
| Denoising | AmpliconNoise122 | |
| DADA28 | ||
| JATAC127 | ||
| UCHIME206 | ||
| Bellerophon207 | ||
| CANGS208,209 | ||
| Databases | SILVA125 | |
| Greengenes94 | ||
| Ribosomal Database Project (RDP)210 | ||
| Unite126 |