Table 1.
List of classifier, target gene, sample (mock community or complex environmental), database and citation for MinION studies investigating microbial systems. ‘X’ indicates yes for column (i.e. analyzed a mock community?) or a linear correlation coefficient >0.69. ‘O’ indicates a linear correlation coefficient <0.25.
| Classifier | Sequence | Mock | Complex sample | GUI | Quantifiable | Database | Reference |
|---|---|---|---|---|---|---|---|
| BLASR, LAST | 16S rRNA gene | X | Self reference | Kilianski et al. 2015 | |||
| BLAST-Discontiguous MegaBlast | rRNA operon | Farm soil, bioreactor | X | X | NCBI 16S rRNA | Kerkhof et al. 2017 | |
| BLAST-Discontiguous MegaBlast | rRNA operon | Human respiratory samples | X | X | EZ BioCloud | Ibironke et al. 2020 | |
| BLAST-Discontiguous MegaBlast | rRNA operon | Mouse feces | X | NCBI 16S rRNA | Dowden et al. 2020 | ||
| BLASTn, Mothur | 16S rRNA gene | X | X | Self reference | Calus, Ijaz and Pinto 2018 | ||
| BLASTn | 16S rRNA gene | X | X | X | Customized SILVA DB | Li et al. 2016 | |
| BLASTn, Centrifuge | 16S rRNA gene | X | Human pleural biopsy | X | NCBI RefSeq, GenomeSync | Mitsuhashi et al. 2017 | |
| BLASTn, MG-RAST | Genomic DNA | Arctic soil/isolates | X | NCBI nr/nt, MG-RAST | Goordial et al. 2017 | ||
| BLASTn, minimap2 | Genomic DNA | X | Human neonate feces | X | X | NCBI nr/nt, Self reference | Leggett et al. 2020 |
| BLASTp | Genomic DNA | Caulerpa ashmeadii holobiont | X | NCBI nr/nt | Sauvage et al. 2019 | ||
| BLAST2GO | 16S rRNA gene | Coastal seawater | X | NCBI nr/nt | Curren et al. 2019 | ||
| Burrows–Wheeler Aligner | Genomic DNA | X | O | Self reference | Sevim et al. 2019 | ||
| Centrifuge | 18S-ITS-28S | X | Coastal seawater | Self reference | Hatfield et al. 2020 | ||
| Centrifuge, Kraken, Kraken2, | Genomic DNA | X | X | Precompiled DB | Leidenfrost et al. 2020 | ||
| Centrifuge, Kraken, WIMP | Genomic DNA | X | X | NCBI RefSeq | Deshpande et al. 2019 | ||
| Centrifuge, Kraken2 | REP-PCR | Isolates | Precompiled DB | Krych et al.2019 | |||
| CosmID, MG-RAST | Genomic DNA | Riverine samples | Proprietary DB, MG-RAST | Hamner et al. 2019 | |||
| EPI2ME | 16S rRNA gene | X | Fresh water samples | X | NCBI RefSeq | Acharya et al.2019 | |
| EPI2ME | 16S rRNA gene | Human cerebral/spinal fluid | NCBI RefSeq | Hong et al.2020 | |||
| EPI2ME | Genomic DNA | X | Human respiratory samples | X | X | NCBI RefSeq, ARMA | Yang et al.2019 |
| EPI2ME, GraphMap, Mothur | 16S rRNA gene | X | X | NCBI 16S rRNA | Winand et al. 2020 | ||
| Epi2ME, Kraken, MG-RAST, One Codex | Genomic DNA | X | O | NCBI RefSeq | Brown et al. 2017 | ||
| EPI2ME, minimap2 | rRNA operon | X | Dog skin | X | X | NCBI RefSeq, rRNA operon DB | Cuscó et al. 2019 |
| EPI2ME, Centrifuge | Genomic DNA | Swabs from oil paintings | X | NCBI RefSeq | Pinar et al. 2020 | ||
| GenomeSync Tool Kit, custom script | 16S rRNA gene | X | O | GenomeSync DB, NCBI DB | Kai et al. 2019 | ||
| Kraken2, MG-RAST, One Codex | Genomic DNA | Riverine samples | Custom reference DB | Reddington et al. 2020 | |||
| LAST | 16S rRNA gene | Mouse feces | GreenGenes DB | Shin et al. 2016 | |||
| LAST | 16S rRNA gene | X | Alexandrium tamarens phylosphere | X | SILVA DB | Shin et al.2018 | |
| LAST | rRNA operon | X | rRNA operon DB | Benitez-Paez and Sanz 2017 | |||
| LAST, Centrifuge | Genomic DNA | Wastewater | X | SARG DB, NCBI nr/nt DB | Che et al.2019 | ||
| LAST,QIIME | 16S rRNA gene, HPV gene | Human cervical sample | GreenGenes DB | Quan et al. 2019 | |||
| Metapathways, MG-RAST | Genomic DNA | Polar sediments, cultures | NCBI 16S rRNA, EZ BioCloud | Millan-Aguinaga et al. 2019 | |||
| MG-RAST | Genomic DNA | Riverine sediments | MG-RAST DB | Samson et al. 2019 | |||
| RDP Classifer, QIIME | 16S rRNA gene | Emergency medical service vehicles | GreenGenes DB | Sheahan et al. 2019 | |||
| SINA aligner | 16S rRNA gene | X | SILVA DB | Benitez-Paez, Portune and Sanz 2016 | |||
| Usearch | Genomic DNA | Stormwater | Custom Human Gut DB | Hu et al. 2018 |