Table 3.
Comparative workflow of the four most commonly used bioinformatics pipeline for analyzing metagenomic datasets.
| EBI | MGRAST | QIIME/QIIME 2 | MOTHUR | |
|---|---|---|---|---|
| License | Free open-source | Free open-source | Free open-source | Free open-source |
| Implementation (release candidate) | Python | Python | Python | C++ |
| Current Version available (March 2018) | 4.1 | 4.0.3 | 1.9.1 and 2017.6.0, respectively | 1.39.5 |
| Website | http://www.ebi.ac.uk/metagenomics | http://metagenomics.anl.gov/ | http://qiime.org/ and https://qiime2.org/ | http://www.mothur.org/ |
| Primary Usage | GUI | GUI | CL and GUI, respectively | CL |
| Amplicon data Analysis | Yes | Yes | Yes | Yes |
| Whole genome shotgun analysis | Yes | Yes | Yes but only experimental | No |
| Sequencing technology compatibility | Sanger, PacBio, Ion Torrent, Illumina, Nanopore | Sanger, PacBio, Ion Torrent, Illumina, Nanopore | Sanger, PacBio, Ion Torrent, Illumina, Nanopore | Sanger, PacBio, Ion Torrent, Illumina, Nanopore |
| Quality control | Yes | Yes | Yes | Yes |
| 16S rRNA gene Databases searched | Silva, Rfam, MAPSeq, Pfam, TIGRFAM, Prints, Prosite patterns, Gene 3d | Silva, M5RNA, RDP and Greengenes | Greengenes, RDP, Siva and Unite | RDP, Greengenes Silva and Unite |
| Alignment method | PyNAST, MUSCLE, INFERNAL | BLAT | PyNAST, MUSCLE, INFERNAL | Needleman-Wunsch, Blastn, Gotoh |
| Taxonomic assignment | UCLUST, BLAST, Mothur, RDP | BLAT | UCLUST, BLAST, Mothur, RDP | Wang/RDP approach |
| Clustering algorithm | UCLUST, BLAST Mothur, CD-HIT | UCLUST | UCLUST, BLAST Mothur, CD-HIT | Mothur, CD-HIT and adapts DOTUR |
| Diversity analysis | Alpha and beta | Alpha | Alpha and beta | Alpha and beta |
| Phylogenetic Tree | YES | YES | FastTree | Clear cut algorithm |
| Visualization | T, BC, PC, HM, SC, PCA, Krona and Circos | T, BC, PC, HM, SC, PCA, Krona and Circos | T, BC, PC, HM, SC, PCA | T, BC, PC, HM, SC, PCA, Dendrograms, Venn diagrams |
| Submitted projects as on March 2018 | Total: 1,653 Public: 1,503 Private:151 |
Total: 3,24,846 Public:52,615 Private:272,231 |
NA | NA |
BC, Bar-Charts; BLAT, Blast like Alignment Tool; CL, Command Line; EBI, European Bioinformatics Institute; GUI, Graphical User Interface; HM, Heat Map; MGRAST, Metagenomic Rapid Annotations using Subsystems Technology; OUT, Operational Taxonomic Unit; PC, Pie-Charts; PCA, Principal Component Analysis; QIIME, Quantitative Insights into Microbial Ecology; RDP, Ribosomal Database Project; SC, Stacked Columns; T, Tabulation.