arg_ranker

arg_ranker evaluates the risk of ARGs in genomes and metagenomes

Install

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

Please make sure to install arg_ranker >= v3

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

Requirement

• python 3
• diamond: conda install -c bioconda diamond=2.1.6 (https://github.com/bbuchfink/diamond)
• blast+: conda install -c bioconda blast (https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
• For metagenomes:
  • kraken2: conda install -c bioconda kraken2(https://github.com/DerrickWood/kraken2/wiki)
    • to compute the abundance of ARGs as copy number of ARGs per bacterial cell (recommended)
      • download the kraken2 standard database (50 GB of disk space): kraken2-build --standard --db $KRAKENDB \ where $KRAKENDB is your preferred database name/location
      • MicrobeCensu: git 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)
    • to compute the abundance of ARGs as copy number of ARGs per 16S
      • download the kraken2 16S database (73.2 MB of disk space): kraken2-build --db $DBNAME --special greengenes

How to use it

• put all your genomes (.fa or .fasta) and metagenomes (.fq or .fastq) into one folder ($INPUT)
• run arg_ranker -i $INPUT (genomes only)
• run arg_ranker -i $INPUT -kkdb $KRAKENDB (genomes/metagenomes + kraken2 standard database)
  • or run arg_ranker -i $INPUT -kkdb $KRAKENDB -kkdbtype 16S (kraken2 16S database)
• run sh arg_ranking/script_output/arg_ranker.sh

Output

• Sample_ranking_results.txt (Table 1)

  • arg_ranker = 3.4 (SARGv3)
  • python >= 3.5
  • diamond = 2.1.6 - recommended
  • blast = 2.13.0
  • kraken2 = 2.1.2 - 16Gb database

  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)

  • arg_ranker = 3.0.2 (SARGv1)
  • python >= 3.5
  • diamond = 0.9.36 - not recommended
  • blast = 2.13.0
  • kraken2 = 2.1.2 - 16Gb database

  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

• Please note that minor changes within ~two-fold of the Total_abu caused by different diamond and kraken versions can be considered reasonable :)

1. Rank_I_per - Unassessed_per: percentage of ARGs of a risk Rank\ Total_abu: total abundance of all ARGs
2. For genomes, we output the copy number of ARGs detected in each genome.
3. For metagenomes, we compute the abundance of ARGs as the copy number of ARGs divided by the bacterial cell number or 16S copy number in the same metagenome.\ If you downloaded the kraken2 standard database, we compute the copy number of ARGs divided by the bacterial cell number.\ If you downloaded the kraken2 16S database, we compute the copy number of ARGs divided by the 16S copy number.\ The copy number of ARGs, 16S, and bacterial cells were computed as the number of reads mapped to them divided by their gene/genome length.
4. We compute the contribution of each ARG risk Rank as the average abundance of ARGs of a risk Rank divided by the average abundance of all ARGs\ Rank_I_risk - Unassessed_risk: the contribution of ARGs of a risk Rank\ Rank_code: a code of contribution from Rank I to Unassessed

• Sample_ARGpresence.txt:\ The abundance, the gene family, and the antibiotic of resistance of ARGs detected in the input samples

Test

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)

Metadata for your samples (optional)

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).

Copyright

Dr. An-Ni Zhang (MIT), Prof. Eric Alm (MIT), Prof. Tong Zhang* (University of Hong Kong)

Citation

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).

Contact

anniz44@mit.edu or caozhichongchong@gmail.com

Acknowledgement

Special thanks to LeabaeL for their great help in testing various versions of arg_ranker and diamond!