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Resistance Gene Identifier (RGI) (version 5.2.1)
input file must be in either FASTA (contig and protein) or gzip format e.g myFile.fasta, myFasta.fasta.gz
specify data input type (default = contig)
specify alignment tool (default = BLAST)
include loose hits in addition to strict and perfect hits
use for short contigs to predict partial genes
specify a data-type (default = NA)

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

  1. Select your input sequence (in FASTA format).
  2. Select your input type (CONTIG or PROTEIN).
  3. Select your alignment tool (DIAMOND or BLAST).
  4. Specify if you want to include loose hits (YES or NO).
  5. Specify if you want to remove temporary files (YES or NO).
  6. Specify if you want to low quality predictions (YES or NO).
  7. Select your data type (WGS, PLASMID, CHROMOSOME or NA).
  8. 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