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How do I access a database?

Section on Connecting to the databases with relevant links
a magnifier zooming in word database

We have just covered a range of databases that contain bacterial AMR mechanisms and you have heard about their strengths and weaknesses. In this section we are going to cover how you might go about accessing these catalogues and leverage their contents.

How do I access a database?

You can download each of the three major AMR databases described earlier as standalone collections. The collections contain various fasta files, containing gene sequences and text files. However, the utility of these databases is best realised via the accompanying tool.

AMR database Download database files
NCBI AMRFinder https://github.com/ncbi/amr/wiki/AMRFinderPlus-database#availability
ResFinder https://github.com/cadms/resfinder/tree/master?tab=readme-ov-file#databases
CARD https://card.mcmaster.ca/download

ResFinder and CARD databases have both command line based tools as well as web-based portals which can be used to access and query the catalogues. In general, the command-line tools (CLI) allow for analysis of larger datasets, more flexibility in settings and may include functionality not included in the web-portals. However, the web-portals are easy to access, are maintained and provide straightforward access to the AMR catalogues.

Often the web-portals do provide capacity to query multiple sequences and sequence types, but this may be limited compared to the CLI tools. NCBI AMRFinder has many resources to gain insights into genes and mechanisms and to query publicly available genomes. NCBI AMRFinder has a stand alone CLI tool called amrfinderplus and is also implemented in other CLI tools including abricate and abritAMR. All of these are available as wrappers and able to be implemented in the Galaxy bioinformatics web-based platform.

Please find the summary of tools with corresponding links in table below:

AMR Database Tool Access to Web-portal Documentation for CLI
CARD RGI https://card.mcmaster.ca/analyze/rgi https://github.com/arpcard/rgi
NCBI AMRFinder AMRFinderPlus, abricate, abritAMR https://usegalaxy.org.au/ https://github.com/ncbi/amr/wiki
ResFinder Resfinder http://genepi.food.dtu.dk/resfinder https://github.com/cadms/resfinder
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