Find Resistance with Nucleotide Database
The Find Resistance with Nucleotide Database tool is designed for resistance typing of de novo-assembled contig sequences.
Find Resistance with Nucleotide Database is inspired by [Zankari et al., 2017] and uses BLAST for identification of acquired antimicrobial resistance genes within whole-genome sequencing (WGS) data.
Nucleotide resistance databases for use with the tool can be downloaded using Download Resistance Database (Download Resistance Database).
To run the tool, go to:
Tools | Microbial Genomics Module (
) | Drug Resistance Analysis (
) | Find Resistance with Nucleotide Database (
)
Select the input genome or contigs (figure 13.3).
Figure 13.3: Pre-assembled and complete- or partial genomes simple contig sequences may be used as input for resistance typing.
You can then specify the settings for the tool (figure 13.4).
Figure 13.4: Select database and settings for resistance typing.
- Database Select a nucleotide resistance database.
- Minimum Identity % is the threshold for the minimum percentage of nucleotides that are identical between the best matching resistance gene in the database and the corresponding sequence in the genome.
- Minimum Length % reflect the percentage of the total resistance gene length that a sequence must overlap a resistance gene to count as a hit for that gene. Here represented as a percentage of the total resistance gene length.
- Filter overlaps: will perform extra filtering of results per contig, where one hit is contained by the other with a preference for the hit with the higher number of aligned nucleotides (length * identity).
The output of the Find Resistance with Nucleotide Database tool is a table listing all the possible resistance genes and predicted phenotypes found in the input genome or contigs, as well as additional information such as degrees of similarity between the gene found in the genome and the reference (% identity and query /HSB values) and the location where the gene was found (contig name, and position in the contig). Depending on the type of database used, additional columns with link to resources may also be present in the table. To add the obtained resistance types to your Result Metadata Table, see the section Extend Result Metadata Table.