Table 1.
Tools for analysing antibiotic resistance from genomes and metagenomes.
| Tool | Tool type | Database-link | Access | Approach | Status | Input description | Requirements | References |
|---|---|---|---|---|---|---|---|---|
| AMRFinderPlus | Detection-database-based | Reference Gene Catalog | Web and standalone | NA; EA; Assembly-based and read based tool | Active | Protein search, protein.fa and nucleotide | HMMER, BLAST+, Linux, and Perl | [78] |
| ResFinder | Detection-database-based | resfinder_db | Web and standalone | NA; EA; Assembly-based and read based tool | Active | Whole genome sequencing, isolate or annotated genome, preassembled partial, complete genomes, reads | [79] | |
| PointFinder | Detection-database-based | Pointfinder_db | Web and standalone | NA; EA; Assembly-based and read based tool | Active | Sequence file in FASTA | BioEdit platform (http://www.mbio.ncsu.edu/bioedit/ | [80] |
| Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT) | Detection-database-based | ARG-ANNOT | Standalone | NA; EA; Assembly-based and read based tool | Active | Analysing genomes, genomes assemblies, metagenomic contigs or proteomes | Prodigal, DIAMON | [81] |
| The Resistance Gene Identifier (RGI) | Detection-database-based | CARD | Web and standalone | NA; EA; Assembly-based and read based tool | Active | Metagenomic | R | [82] |
| Online Analysis Pipeline for Anti-biotic Resistance Genes Detection (ARGs-OAP v2) | Detection-database-based | Web and standalone | NA; EA; Assembly-based and read based tool | Active | Sequence reads, allele db, gene db | python (v2.7.5) | [83] | |
| Short Read Sequence Typing for Bacterial Pathogens (SRST2) | Detection-database-based | Standalone | NA; EA Read-based tool | Active | Metagenomic and db | Unix server with ~2 GB of disk space for reference data 2X the input FASTQ file size in both RAM and disk space for temporary file storage :Perl , r, usearch, bwa, tophat incl., bam2fastx, samtools incl. bcftools and vcfutils.pl, ncbi blast, seqtk | [84] | |
| Search Engine for Antimicrobial Resistance (SEAR) | Detection-database-based | Web and standalone | NA; EA Read-based tool | Last update 2017 | Sequence reads | Linux | [85] | |
| Antimicrobial Resistance Identification By Assembly (ARIBA) | Detection-database-based | ARG-ANNOT, CARD, MEGAres and ResFinder | Standalone | NA; EA; Assembly-based and read based tool | Active | Sequence reads | Linux | [86] |
| SSTAR | Detection-database-based | SEED (annotator), AMR-related proteins that have been curated at ARDB and CARD | Standalone | NA; EA assembly-based and read based tool | Active | Two sequence files in FASTA format, one containing the bacterial genome assembly and the other the AR gene collection | NS | [73] |
| AdaBoost (PATRIC) | Detection and classification | Web | ML; EA Read-based tool | Active | Whole genome sequencing reads | NA | [87] | |
| PARGT | Detection-database-based | Standalone | NA | Active | Protein sequences | R and Python | [88] | |
| Resfams | Databased and AMR protein predictor | Resfams | Web and standalone | NA | Last update 2018 | NA | None | [89] |
| Antibiotic Resistance Genes Database (ARDB) | Database | ARDB | Web and standalone | NA | Available | NA | None | [90] |
| NCBI Bacterial Antimicrobial Resistance Reference Gene Database (BARRGD) | Database | PRJNA313047 | Web | NA | Active | NA | None | |
| NCBI Pathogen Detection | Database | Pathogens | Web | NA | Active | NA | None | |
| National Database of Antibiotic Resistant Organisms (NDARO) | Database | NDARO | Web | NA | Active | NA | None | |
| Isolates Browser | Database | Insolates Browser | Web | NA | Active | NA | None | |
| RefSeq | Database | refseq | Web | NA | Active | NA | None | [91] |
| How to Request New Alleles for Beta-Lactamase, MCR, and Qnr Gene | Database | Home page | Web | NA | Active | NA | None | |
| Microbial Browser for Identification of Genetic and Genomic Elements (MicroBIG-E) | Database | microbigge | Web | NA | Active | NA | None | |
| HMDARG | Database | HMDARG | Web | Assembly-based tool and hierarchical classification | Active | Raw sequence encoding | None | [120] |
NA: Not applicable EA: Exploratory approaches.