Commit 2f5c542d authored by Laura Denies's avatar Laura Denies
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Update README.md

parent d4b58eb6
......@@ -35,4 +35,7 @@ Finally for LINUX system to allow diamond to be executed go to ./bin within the
chmod +x diamond
For more explanations on the deepArg configuration see the deepArg documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
# 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.
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