Frequently asked questions
Which genomes are searched?
Tool 1 uses the tool_1.nf workflow to query the selected genomes in the input_tool1 folder.
Additional, the tool_1_EVERYTHING.nf workflow can be used to search ALL the genomes in the LIBRARY folder.
Which genomes are in the LIBRARY folder?
All genomes assembled by the Core appliance can be found in the Tool 1 LIBRARY folder. This is updated manually by running populate_inputs.sh. Instructions on how to run populate_inputs.sh can be found here. The files are hard linked, so they are not duplicated on the server.
Additionally, reference genomes can be added to this folder.
Which databases are available?
The available databases are:
| Database | command | Database contents |
|---|---|---|
| ARG-ANNOT | argannot |
Antibiotic resistance genes |
| CARD | card |
The Comprehensive Antibiotic Resistance Database |
| EcOH | ecoh |
Serotyping of E. coli |
| ecoli_vf | ecoli_vf |
Escherichia coli virulence factors. Included VFDB and more E.coli specific genes |
| NCBI BARRGD | ncbi |
NCBI Bacterial Antimicrobial Resistance Reference Gene Database |
| PlasmidFinder | plasmidfinder |
In silico detection and typing of plasmids |
| ResFinder | resfinder |
ResFinder identifies acquired antimicrobial resistance genes |
| VFDB | vfdb |
Virulence factor database |
What are the different folders for?
The Tool 1 file system contains the following folders:
| Directory name | Description of contents |
|---|---|
| LIBRARY | The sequence files (.fa) for all sequenced isolates |
| input_tool1 | All assemblies (*.fa) in this directory will be tested by tool_1. |
| output_tool1 | Your output data will be deposited here in subdirectories named xxx_i(yy)_c(zz)_YYYY-MM-DD_HH:MM, where xxx is the database, yy is the identity and zz is the coverage. This is followed by the date and time the run was started. |
| work | The Nextflow working directory. |
How do you run Tool 1?
Running Tool 1 is straight-forward.
Briefly, once you have accessed Tool 1 and placed the assemblies you wish to test into the input folder all you need to do is enter a single command and the results will be deposited in the output folder.
What documents are made by Tool 1?
In the run output folder, Tool 1 deposits the documents in 2 sub-folders: isolate and summary.
In the isolate folder there will be a results file for each strain. In the summary folder there will be a single document summarising all ‘hits’ results.
Additionally, in the run output folder itself you will find run_parameters.txt. This text document lists:
- the database used (`xxx`)
- the number of sequences in the database,
- the date the database was downloaded,
- the version number of the software (abricate),
- the minimum DNA %identity (`yy`) and
- the minimum DNA %coverage (`zz`).
Ignore help=false. This is an expected byproduct of the help/usage message.
How do you view the output files?
You can open the files in Excel. The output files are in .tab format.
The run_parameters.txt document can be opened in any text editor.
Can I change the settings of Tool 1?
Yes, you can modify the two different settings: identity and coverage. Using the default settings there must be a minimum DNA identity of 80%, and a minimum DNA coverage of 80% for a match to be recorded. These can be altered when you set Tool 1 to run.
For all runs, the settings are recorded in the name of the newly created output folder, e.g. the results of a run on May 21st 2021 started at 1.30 pm using the resfinder database and default settings will be stored in this folder: resfinder-i80-c80__2021-05-21_13:15/.
Where can I find further information about Tool 1?
Tool 1 uses the ABRicate software tool. It was developed by Torsten Seemann and Björn Grüning in Melborne, Australia. The ABRicate information page can be found here on GitHub.