Commit a8e3e188 authored by Laura Denies's avatar Laura Denies
Browse files


parent 85731b76
......@@ -15,15 +15,15 @@ PathoFact provides the conda environments with the dependencies needed to run th
Some of the tools itself, however, still need to be installed.
The following tools need to be installed by the user itself and the path to the tools adjusted within the config.yaml file:
* HMMER-3.2.1
* singalp-4.1
The following tools can either be installed manually or the script can be run to install automatically:
*deepARG (v1)
*PlasFlow (v1.1)
*VirSorter (v1.0.5)
*DeepVirFinder (v1.0)
* deepARG (v1)
* PlasFlow (v1.1)
* VirSorter (v1.0.5)
* DeepVirFinder (v1.0)
It is recommended to install using the script.
If installed manually make sure that the tools are installed in the folder "scripts" and the pathways matches those within the config.yaml
......@@ -42,10 +42,34 @@ The input to the ViruTox pipeline consists of; (i) an amino acid fasta file of t
Contig and gene names need to correlate with the original names given in the fasta headers. Furhtermore, make sure that no white spaces are present in the fasta headers.
All three input files used by the pipeline for one sample need to be given the same sample name, followed by the suffix .faa (amino acid, gene fasta file), .fna (nucleotide contig fasta file), .contig (table with contig and gene names).
## Run PathoFact
To run PathoFact the sample name is given in the config.yaml file at "input_file". If wanted more than one sample can be run at the simultanously, for example:
* input_file: ["SAMPLE_A","SAMPLE_B"]
* input_file: ["SAMPLE_A","SAMPLE_B"]
In "OUTDIR" the pathway to the samples are given and the PathoFact results are deposited in the same directory.
* input_file: /path/to/samples
In "project" an unique name for your project need to be given, for example:
* project: Project_A_PathoFact
Lastly in the file called "Snakefile" the required workflow can be selected, which give the following options:
* w = 'complete' (run complete pipeline, default setting)
* w = 'Tox' (run only workflow for Toxin prediction)
* w = 'Vir' (run only workflow for Virulence prediction)
* w = 'AMR' (run only workflow for Antimicrobial resistance and mobile genetic element prediction)
To run the snakemake pipeline and example script is given (, but the following is the basics to run the pipeline:
* snakemake -s Snakefile --use-conda -p
alternatively one can adjust the number of threads per job (when analysing bigger files it is advised to run on either multiple "cores" or cores with "more" memory)
* snakemake -s Snakefile -j [number of threads/jobs] --use-conda -p
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