Find Resistance with ShortBRED

This tool allows you to detect and quantify the presence of antibiotic resistance (AR) marker genes by running DIAMOND with a database of peptide marker sequences which represent the genes of interest. The Find Resistance with ShortBRED tool works similarly to the quantify step of ShortBRED, a public bioinformatics pipeline and resource. To learn more about the ShortBRED-Quantify tool [Kaminski et al., 2015], see

Find Resistance with ShortBRED quantifies the presence of Antibiotic Resistance (AR) marker genes in a sample of NGS short reads. It is possible to output a sequence list containing all the input reads which contained a marker (each read in the output is annotated with metadata describing the properties of the marker detected in the read).

Antibiotic Resistance marker databases for use with the tool can be downloaded using Download Resistance Database (Download Resistance Database).

To start the tool, go to:

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Drug Resistance Analysis (Image resistance_folder_closed_16_n_p) | Find Resistance with ShortBRED (Image ar_quantify_16_n_p).

The tool accepts a nucleotide sequence or sequence list as input.

In the next dialog (figure 12.5), several parameters are available:

Image shortbred
Figure 12.5: References and search parameters.

The Find Resistance with ShortBRED tool will output a resistance abundance table, a result summary table, an optional report, and an optional sequence list.

The result summary table provides an overview of all the resistance phenotypes in the applied database and reports the number of identified resistance genes and markers, and number of reads assigned to each phenotype.

The optional report output contains general information about the input sample, the marker database used and a short result summary.

The optional sequence list output contains all reads from the input sample which were found to contain one of the AR marker sequences. Each read in the sequence list is annotated with metadata describing the properties of the marker detected in the read.