Main tool : ResFinder
Additional tools:
- kma 1.4.14
- ResFinder database 2.3.1
- PointFinder database 4.1.0
- disinfinder database 2.0.1
Alternatively available as a webtool here: https://cge.cbs.dtu.dk/services/ResFinder/
Full documentation: https://bitbucket.org/genomicepidemiology/resfinder/src/master/
ResFinder identifies acquired genes and/or finds chromosomal mutations mediating antimicrobial resistance in total or partial DNA sequence of bacteria.
WARNING : The executable has changed!
# run ResFinder on raw reads (FASTQs)
python3 -m resfinder -ifq /data/sample_1.fastq /data/sample_2.fastq \
-o /data/resfinder-results-fastq-input \
-acq -l 0.9 -t 0.9 \
-c -s "Escherichia coli"
# run ResFinder on assembly FASTA
python3 -m resfinder -ifa /data/sample.fasta \
-o /data/resfinder-results-fasta-input \
-c \
-acq -l 0.9 -t 0.9 \
--species "Escherichia coli" \