Frequently asked questions
Description of the output files:
The output files are named *.candidate_unique.fa.
Where * is the isolate’s ‘friendlyName’, originally defined in the Core index file.
There is one file per isolate, subject to identification of unique stretches. If no unique ORFs
re identified then no output file will be returned.
The contents of the output files will be in fasta format as follows:
>contig ID of longest unique ORF
DNA sequence
>contig ID of second longest unique ORF
DNA sequence
...
>contig ID of tenth longest unique ORF
DNA sequence
What are the different folders for?
The Tool 4 file system contains the following folders:
| Directory name | Description of contents |
|---|---|
| input_tool4 | All assemblies (*.fasta) in this directory will be tested by tool_4. |
| output_tool4 | Your output data will be deposited here in subdirectories named YYYY-MM-DD_HH:MM. |
| work | The Nextflow working directory. |
How do you run Tool 4?
Running Tool 4 is straight-forward.
Briefly, once you have accessed Tool 4 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. You can use these to design primers.
How do you view the output files?
You can open the files in any text editor.
Can I change the settings of Tool 4?
Yes, you can modify the two different settings: identity and eValue. 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 4 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 will be stored in this folder: 2021-05-21_13:15/.
Where can I find further information about Tool 4?
Tool 4 was developed in collaboration between Amy Baldwin and Matt Bull.
It utilises the prodigal gene prediction software, ncbi's blast+, samtools, bbmap and seqtk.
Further information about these tools can be found by following the links above.