arg_ranker evaluates the risk of ARGs in genomes and metagenomes
experimental version using most updated ARG database (SARGv3)\
pip install arg_ranker
\
Long term support version using the same ARG database in the publication (SARGv1)\
pip install arg-ranker==3.0.2
To all users,\
We have noticed an error of arg_ranker.v2 when reporting the total ARG abundance in metagenomes.\
If the total abundance is used in your research, please update arg_ranker to v3 and re-run your metagenomes (arg_ranker -i $INPUT -kkdb $KRAKENDB
).\
Alternatively, you can fix arg_ranker.v2 by replacing its original ARG_table.sum.py with ARG_table.sum.py\
and re-run the last two commands in arg_ranker.sh python $PATH_to_arg_ranker/bin/ARG_table.sum.py -i ...
and arg_ranker -i ...
.\
You can find the path to ARG_table.sum.py in arg_ranker.sh.\
Note that this ARG_table.sum.py is only meant for fixing arg_ranker.v2 and the results of arg_ranker.v2.\
Please do not replace ARG_table.sum.py in arg_ranker.v3 with this ARG_table.sum.py.\
We are really sorry about this inconvenience.\
Please feel free to reach out to anniz44@mit.edu if you have any questions.
To check installed version pip show arg_ranker
\
To upgrade pip install arg_ranker --upgrade
conda install -c bioconda diamond=2.1.6
(https://github.com/bbuchfink/diamond)conda install -c bioconda blast
(https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)conda install -c bioconda kraken2
(https://github.com/DerrickWood/kraken2/wiki)
kraken2-build --standard --db $KRAKENDB
\
where $KRAKENDB is your preferred database name/locationgit clone https://github.com/snayfach/MicrobeCensus && cd MicrobeCensus && python setup.py install
to estimate the average genome size for metagenomes.
(https://github.com/snayfach/MicrobeCensus)kraken2-build --db $DBNAME --special greengenes
arg_ranker -i $INPUT
(genomes only)arg_ranker -i $INPUT -kkdb $KRAKENDB
(genomes/metagenomes + kraken2 standard database)
arg_ranker -i $INPUT -kkdb $KRAKENDB -kkdbtype 16S
(kraken2 16S database)sh arg_ranking/script_output/arg_ranker.sh
Sample_ranking_results.txt (Table 1)
Sample | Rank_I_per | Rank_II_per | Rank_III_per | Rank_IV_per | Unassessed_per | Total_abu | Rank_code | Rank_I_risk | Rank_II_risk | Rank_III_risk | Rank_IV_risk | ARGs_unassessed_risk | note1 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
WEE300_all-trimmed-decont_1.fastq | 6.6E-02 | 2.1E-02 | 2.2E-01 | 6.9E-01 | 0.0E+00 | 5.5E+00 | 3.1-1.3-1.1-0.9-0.0 | 3.1 | 1.3 | 1.1 | 0.9 | 0.0 | hospital_metagenome |
EsCo_genome.fasta | 7.1E-02 | 0.0E+00 | 2.1E-01 | 7.1E-01 | 0.0E+00 | 1.4E+01 | 3.3-0.0-1.1-0.9-0.0 | 3.3 | 0.0 | 1.1 | 0.9 | 0.0 | E.coli_genome |
Sample_ranking_results.txt (Table 1)
Sample | Rank_I_per | Rank_II_per | Rank_III_per | Rank_IV_per | Unassessed_per | Total_abu | Rank_code | Rank_I_risk | Rank_II_risk | Rank_III_risk | Rank_IV_risk | ARGs_unassessed_risk | note1 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
WEE300_all-trimmed-decont_1.fastq | 4.6E-02 | 0.0E+00 | 6.8E-02 | 7.5E-01 | 1.3E-01 | 1.9E+00 | 1.5-0.0-0.4-1.7-0.4 | 1.5 | 0.0 | 0.4 | 1.7 | 0.4 | hospital_metagenome |
EsCo_genome.fasta | 0.0E+00 | 0.0E+00 | 2.4E-01 | 7.6E-01 | 0.0E+00 | 2.1E+01 | 0.0-0.0-1.6-1.7-0.0 | 0.0 | 0.0 | 1.6 | 1.7 | 0.0 | E.coli_genome |
run arg_ranker -i example -kkdb $KRAKENDB
\
run sh arg_ranking/script_output/arg_ranker.sh
\
The arg_ranking/Sample_ranking_results.txt should look like Table 1 (using kraken2 standard database)
arg_ranker can merge your sample metadata into the results of ARG ranking (i.e. note1 in Table 1).\ Simply put all information you would like to include into a tab-delimited table\ Make sure that your sample names are listed as the first column (check example/metadata.txt).
Dr. An-Ni Zhang (MIT), Prof. Eric Alm (MIT), Prof. Tong Zhang* (University of Hong Kong)
Zhang, AN., Gaston, J.M., Dai, C.L. et al. An omics-based framework for assessing the health risk of antimicrobial resistance genes. Nat Commun 12, 4765 (2021). https://doi.org/10.1038/s41467-021-25096-3 Correction: bacA is a bacitracin resistance gene, not a beta-lactamase (Fig 3).
anniz44@mit.edu or caozhichongchong@gmail.com
Special thanks to LeabaeL for their great help in testing various versions of arg_ranker and diamond!