amr_curation

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AMR Curation

Actively monitored by the CARD Curation Team.

A number of databases and software tools exist for DNA sequence-based investigation of antimicrobial resistance (see Boolchandani, D'Souza, & Dantas. 2019. Sequencing-based methods and resources to study antimicrobial resistance. Nat Rev Genet <https://www.nature.com/articles/s41576-019-0108-4>). We encourage researchers, software developers, and AMR data curators to use this repository to submit, discuss, and resolve AMR curation issues. Anyone with a GitHub account can submit an issue <https://github.com/arpcard/amr_curation/issues>. AMR software developers or database curators are welcome to join the repository as Contributors <https://github.com/arpcard/amr_curation/graphs/contributors>_ to share files, data, & code as well as add documentation (send request to [email protected] or submit a GitHub issue <https://github.com/arpcard/amr_curation/issues>_).

If you are submitting a question or correction <https://github.com/arpcard/amr_curation/issues>_ about AMR data in a particular database, please indicate the database in your submission. If your question or issue is about software, please use the software's own repository or email address to report the problem.

We also maintain the amr_curation-l <https://mailman.mcmaster.ca/mailman/listinfo/amr_curation-l>_ email mailing list for discussion of AMR curation issues if you prefer to this over GitHub. Lastly, we maintain some online resources, please help us keep these up to date:

• Wikipedia's list of Antimicrobial Resistance databases <https://en.wikipedia.org/wiki/List_of_biological_databases#Antimicrobial_resistance_databases>_
• Google Spreadsheet of AMR Databases and Software <https://docs.google.com/spreadsheets/d/1psHogF0rZIIq9AXbFfjQNYVXoOVHEYPOi9CYLvtO04U/edit?usp=sharing>_

.. image:: images/volunteers.jpg

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Anna-Lisa Nguyen & William Huynh amr_curation Project Leads at CARD

Participant List

• Comprehensive Antibiotic Resistance Database <http://card.mcmaster.ca>_ | @arpcard
• NCBI Beta-Lactamase Alleles <https://www.ncbi.nlm.nih.gov/bioproject/305729>_ and Bacterial Antimicrobial Resistance Reference Gene Database <https://www.ncbi.nlm.nih.gov/bioproject/PRJNA313047>_
• Public Health Agency of Canada (PHAC)'s IRIDA AMR Detection Pipeline <https://github.com/phac-nml/irida-plugin-amr-detection>_ | @apetkau
• ResFinder & PointFinder <https://cge.cbs.dtu.dk/services/ResFinder/>_, database and software for identification of acquired antimicrobial resistance genes and/or chromosomal mutations in total or partial sequenced isolates of bacteria
• Tetracycline and MLS Nomenclature Database <https://faculty.washington.edu/marilynr/>_, maintained by dr. Marilyn Roberts | [email protected]
• ARGDIT <https://github.com/phglab/ARGDIT>_, a toolkit to validate and consolidate antimicrobial resistance gene databases | @jimmykhchiu
• AMRTime <https://github.com/beiko-lab/AMRtime>_, a tool to predict the presence of antimicrobial resistance in clinical metagenomes | @fmaguire
• MEGARes <https://megares.meglab.org>_, an Antimicrobial Database for High-Throughput Sequencing
• AmrPlusPlus software <https://github.com/cdeanj/amrplusplus>_, a high-throughput analysis pipeline to identify and characterize resistance genes from metagenomic sequence data | @cdeanj
• AMR++ Shiny <https://github.com/lakinsm/amrplusplus-shiny>_, statistics interface for metagenomic resistome and microbiome analyses | @lakinsm
• Agriculture and Agri-Food Canada | @ropolomx
• Groot <https://github.com/will-rowe/groot>_ & BabyGroot <https://github.com/will-rowe/baby-groot>_ resistome profilers for Graphing Resistance Out Of meTagenomes | @will-rowe
• uCARE <http://e-bioinformatics.net/ucare/>_, a Comprehensive Antibiotic resistance Repository of Escherichia coli | @sauravbsaha
• uCAREChemSuiteCLI <https://github.com/sauravbsaha/uCAREChemSuiteCLI>_ predicts resistome profiles for chemical structures | @sauravbsaha
• Beta-Lactamase DataBase (BLDB) <http://www.bldb.eu/>_ database for biochemical, structural, and sequencing information on beta-lactamases | @iorga
• CBMAR <http://proteininformatics.org/mkumar/lactamasedb/>_ facilitates comprehensive annotation of beta-lactamases and their molecular and biochemical characterizations
• INTEGRALL <http://integrall.bio.ua.pt/>_ web-tool to provide information on integron DNA sequences and genetic arrangements
• PATRIC <https://patricbrc.org/>_ provides integrated data and analysis tools for bacterial infectious disease research and inquiry
• BacMet <http://bacmet.biomedicine.gu.se>_ Antibacterial biocide and metal resistance genes database