Resistance Gene Identifier (RGI)
RGI is used to predict resistome(s) from protein or nucleotide data based on homology and SNP models. The tool uses data from the CARD database.
Usage
- Select your input sequence (in FASTA format).
- Select your input type (CONTIG or PROTEIN).
- Select your alignment tool (DIAMOND or BLAST).
- Specify if you want to include loose hits (YES or NO).
- Specify if you want to remove temporary files (YES or NO).
- Specify if you want to low quality predictions (YES or NO).
- Select your data type (WGS, PLASMID, CHROMOSOME or NA).
- Run the tool.
Output
There are 2 different output files produced by rgi.
summary.txt
A tabular file of all detected resistance genes, one gene per line.
ORF_ID |
Contig |
Start |
Stop |
Orientation |
Cut_Off |
Pass_Bitscore |
Best_Hit_Bitscore |
Best_Hit_ARO |
Best_Identities |
ARO |
Model_type |
SNPs_in_Best_Hit_ARO |
Other_SNPs |
Drug Class |
Resistance Mechanism |
AMR Gene Family |
Predicted_DNA |
Predicted_Protein |
CARD_Protein_Sequence |
Percentage Length of Reference Sequence |
ID |
Model_ID |
AY123251.1_6 # 3575 # 4489 # 1 # ID=1_6;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399 |
AY123251.1_6 |
3575 |
4489 |
+ |
Strict |
500 |
506.908 |
CARB-7 |
83.68 |
3002246 |
protein homolog model |
n/a |
n/a |
penam |
antibiotic inactivation |
CARB beta-lactamase |
ATGC |
MLLYKMCDNQNYGVTYMKFLLV |
MKSLLVFALLMPSVVFASSSKFQSV |
105.56 |
gnl|BL_ORD_ID|589|hsp_num:0 |
1443 |
report.json
A json version of summary.txt.
Help
- usage:
- rgi main [-h] -i INPUT_SEQUENCE -o OUTPUT_FILE [-t {read,contig,protein,wgs}] [-a {DIAMOND,BLAST}] [-n THREADS] [--include_loose] [--local] [--clean] [--debug] [--low_quality] [-d {wgs,plasmid,chromosome,NA}] [-v]
optional arguments:
- -h, --help
- show this help message and exit
- -i INPUT_SEQUENCE, --input_sequence INPUT_SEQUENCE
- input file must be in either FASTA (contig and protein) or gzip format e.g myFile.fasta, myFasta.fasta.gz
- -o OUTPUT_FILE, --output_file OUTPUT_FILE
- output folder and base filename
- -t {read,contig,protein,wgs}, --input_type {read,contig,protein,wgs}
- specify data input type (default = contig)
- -a {DIAMOND,BLAST}, --alignment_tool {DIAMOND,BLAST}
- specify alignment tool (default = BLAST)
- -n THREADS, --num_threads THREADS
- number of threads (CPUs) to use in the BLAST search (default=8)
- --include_loose
- include loose hits in addition to strict and perfect hits
- --local
- use local database (default: uses database in executable directory)
- --clean
- removes temporary files
- --debug
- debug mode
- --low_quality
- use for short contigs to predict partial genes
- -d {wgs,plasmid,chromosome,NA}, --data {wgs,plasmid,chromosome,NA}
- specify a data-type (default = NA)
- -v, --version
- prints software version number