4AN_AMR
Introduction
4AN_AMR (Anti-Microbial Resistance) performs prediction of antibiotic resistace- and virulence-associated gene presence in the reconstructed sequence of the microorganism of interest.
Run Analysis 4AN_AMR
Once the analysis 4AN_AMR has been selected from the run analyses interface, the user will be able to select which bioinformatic tool to use. The available tools are listed below.
For all microorganisms:
- abricate - Mass screening of contigs for antimicrobial resistance or virulence genes
4AN_AMR requires input sequences from de novo assembly or mapping; if the latter are provided, the reference genome that has been used for mapping will also be required.
The input selection UI delivers an advanced input selection mode, to allow selection of all types of supported input files at once.
Accepted inputs can be from:
A link to Check analysis will be created after launching the requested analysis. The system will notify the user after a succesful analysis launch and once execution has ended.
Output directory
Please refer to Cohesive's specific Wiki page for information on file download.
The output directory is available at the link in the download page or at the link presente in the analysis' summary card, and will have the following structure: results > YEAR > ID > 4AN_AMR > DSXXXXXXXX-DTXXXXXX_abricate. The last directory's suffix will be replaced with the name of the chosen tool. At that path there will be 2 directories:
- meta: ("metadata") contains log and configuration files.
- result: contains the analysis' output files.
The table below list files produced by tools available for 3TX_species.
| File | Description | Location |
|---|---|---|
| DSXXXXXXXX-DTXXXXXX_ID_abricate_calls.txt | file with gene alignment results, coverage and database queries | results directory |
| DSXXXXXXXX-DTXXXXXX_ID_abricate.summary | abricate summary file containing gene and its coverage | results directory |
| DSXXXXXXXX-DTXXXXXX_ID_output_abricate_AMR.csv | antibiotic resistance genes summary file | results directory |
| DSXXXXXXXX-DTXXXXXX_ID_output_abricate_VF.csv | virulence genes summary file | results directory |
In the .summary file, for each sample there will also be a number listed in the genes column, which is the value of the horizontal coverage of the associated gene. In case of fragmented genes, multiple semicolon-separated values will be listed, each associated to one of the contigs from de novo assembly that matched the gene.
For more details on abricate output files, please refer to abricate's official manual.
