Table 1.

Comparison of current HPV or virome detection tools

Detection tool	Function	Web based	Input data	Methods of virus identification	De novo assembly	Database
HPViewer	Genotyping and quantification of HPV with non-specific repeats masked.	No	Raw reads	Bowtie2	No	Repeat-masked and homology-masked HPV genomes
HPVDetector	Detecting of HPV and identifying chromosomal integration sites	No	Raw reads	BWA	No	Multiple HPV genomes and human genome
VirusTAP	Identification of viral genome sequences after subtraction of host and bacteria-related reads	Yes	Raw reads	BLAST	Yes	Customized viral nucleotide/protein sequences from the NCBI nt/nr database excluding bacteriophages, human genome, ribosomal RNAs, bacterial genome sequences, the latest host organisms genome sequences
Vipie	Parallel analysis of multiple metagenomic samples for viruses identification	Yes	Raw reads	BLAST	Yes	A custom database with 20 759 viruses, human genome, ribosomal DNA of bacteria, archaea and fungi
VirusScan	Investigation of the viral presence in human tumors	No	Raw reads	BWA	No	A custom virus database containing clustered viral sequences from NCBI NT database, human genome
VIP	One-touch pipeline for metagenomic virus identification	No	Raw reads	Bowtie2	Yes	Virus nucleotide from ViPR, IRD, Refseq viral, DDBJ, EMBL and GenBank, viral protein databases from Refseq, human genome, bacterial genome from GOTTCHA
Metavir2	Viral detection of metagenomics	Yes	Raw reads or contigs	BLAST, HMM	Either	Virus DNA and protein database from RefSeq NCBI taxonomy, kmer frequency pattern, PFAM protein domain database
VirSorter	Metagenomic virus identification in both reference dependent and independent manners	No	Contigs	BLAST, HMM	No	Virus proteins from RefSeq, viral sequences sampled from freshwater, seawater and human gut, lung and saliva, PFAM protein domain database
VirFinder	Identification of viral sequences by k-mer analysis	No	Contigs	k-mer frequency based machine learning	No	Virus k-mer signatures