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 consisting of peptide marker sequences which represent the genes of interest. These marker databases can be downloaded using the tool Download Resistance Database. 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).

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 14.6), several parameters are available:

Image shortbred
Figure 14.6: 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 detected resistance phenotypes. The table reports the number of resistance genes identified, the number of markers and the number of reads for each resistance 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.