Table 1.
Bioinformatic tools and databases for antimicrobial resistant gene (ARG) detection from whole genome sequencing (WGS) or whole metagenome sequencing (WMS) data.
| Name | Type of Tool | Link |
|---|---|---|
| RGI | Assembly-based | https://card.mcmaster.ca/analyze/rgi (accessed on 15 January 2021) |
| CARD | Assembly-based | https://card.mcmaster.ca/ (accessed on 15 January 2021) |
| ARGs-OAP (v2 | Assembly-based | https://galaxyproject.org/use/args-oap/ (accessed on 15 January 2021) |
| ARIBA | Assembly-based | https://github.com/sanger-pathogens/ariba (accessed on 15 January 2021) |
| NCBI–AMRFinder | Assembly-based | https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/ (accessed on 15 January 2021) |
| PointFinder | Assembly-based | https://cge.cbs.dtu.dk/services/ResFinder/ (accessed on 15 January 2021) |
| ShortBRED | Read-based | http://huttenhower.sph.harvard.edu/shortbred (accessed on 15 January 2021) |
| SEAR | Read-based | https://github.com/will-rowe/SEAR (accessed on 15 January 2021) |
| KmerResistance | Read-based | https://cge.cbs.dtu.dk/services/KmerResistance/ (accessed on 15 January 2021) |
| PATRIC | Read-based | www.patricbrc.org (accessed on 15 January 2021) |
| SSTAR | Read-based | https://github.com/tomdemanbio/Sequence-Search-Toolfor-Antimicrobial-Resistance-SSTAR (accessed on 15 January 2021) |
| DeepArgs | Read-based | https://bench.cs.vt.edu/deeparg (accessed on 15 January 2021) |
| GROOT | Read-based | https://github.com/will-rowe/groot (accessed on 15 January 2021) |