Identify phage contigs from metagenomics data.

Input

• Contig sequences in FASTA format
• Optionally own predicted protein sequences can be given (by default the tool will use prodigal and diamond blastp for the prediction)

Output:

A tabular dataset with the following columns:

• Accession: the accession or the name of the input contigs.
• Length: the length of input contigs.
• Pred: virus or non-virus.
• Proportion: the proportion of the proteins that can be aligned to the virus database (from 0 to 1).
• PhaMerScore: the prediction score given by the deep learning model.
• PhaMerConfidence: the confidence of prediction, determined by both Proportion and PhaMerScore (high-confidence, medium-confidence, low-confidence, lower than reject threshold (according to the --reject parameter, default: 0.1)). For the virus with low-confidence or lower than reject threshold, we recommend you to run the contamination task to check their sequence quality.