Gitlab is now using https://gitlab.lcsb.uni.lu as it's primary address. Please update your bookmarks. FAQ.

Commit 09e8c824 authored by Laura Denies's avatar Laura Denies
Browse files

Update README.md

parent 2f5c542d
......@@ -37,5 +37,15 @@ For more explanations on the deepArg configuration see the deepArg documentation
# Usage
The input to the ViruTox pipeline consists of; (i) an amino acid fasta file of translated gene sequences for the prediction of toxins, virulence factors and antimicrobial resistance genes, (ii) a fasta file containing nucleotide sequences of the corresponding contigs for the prediction of MGEs, and (iii) a table consisting of a first column of contig names with the corresponding gene names in the second column to combine predictions. Contig names need to correlate with the original names given in the fasta headers.
##Input configuration
The input to the ViruTox pipeline consists of; (i) an amino acid fasta file of translated gene sequences for the prediction of toxins, virulence factors and antimicrobial resistance genes, (ii) a fasta file containing nucleotide sequences of the corresponding contigs for the prediction of MGEs, and (iii) a tab delimited table consisting of a first column of contig names with the corresponding gene names in the second column to combine predictions.
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).
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"]
In "OUTDIR" the pathway to the samples are given and the PathoFact results are deposited in the same directory.
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment