Table 2.
Bioinformatic tools for virome analyses. Table shows selected bioinformatic tools classified as alignment- or k-mer-based, a brief description and the source.
| Bioinformatic Tool | Description | Source | Reference |
|---|---|---|---|
| Alignment-based | |||
| VIROME | Web-application interface for the classification of Open-Reading Frames (ORF) or assembled data, which receive one classification. | http://virome.dbi.udel.edu | [146] |
| VirusSeeker | Linux-based for the classification of sequences at the nucleotide and amino acid level. It is used for virus characterization and discovery; the latter requires assembled reads. | http://pathology.wustl.edu/virusseeker/index.htm | [147] |
| VirFind | Web-based tool that maps the reads to reference genomes and also performs de novo assembly to get longer contigs to identify known viruses and discover new ones. It performs Blastn and Blastx. | http://virfind.org/j/ | [148] |
| FastViromeExplorer | Pseudo-alignment tool that maps reads to a reference virus database, filters the alignment results based on minimal coverage criteria and reports virus types and abundances along with taxonomic annotation. | https://bench.cs.vt.edu/FastViromeExplorer/ | [149] |
| VirMap | Suitable for low coverage and highly divergent viruses in metagenomic datasets. Uses a mapping assembly algorithm with both nucleotide and amino-acid alignments to build virus-like super-scaffolds. It possesses a taxonomic classification algorithm based on bits-per-base scoring system. | https://github.com/cmmr/VirMAP | [150] |
| EZ-Map | Python-based to filter, align, and analyze viromes from cell-free DNA samples. | https://github.com/dekoning-lab/ezmap | [151] |
| MetaVir2 | Web-application interface that works with assembled reads to perform taxonomy assignments based on available sequences in RefSeq. | http://metavir-meb.univ-bpclermont.fr | [152] |
| Vipie | Web-application capable of analyzing datasets from different studies by performing de-novo assembly, followed by taxonomic classification. | https://binf.uta.fi/vipie/ | [153] |
| ViromeScan | Linux-based application that performs taxonomy classification from raw data. The tool uses hierarchical databases for eukaryotic viruses to assign reads to viral species. | http://sourceforge.net/projects/viromescan/ | [154] |
| Vanator | Perl-based pipeline designed for metagenomics and virus discovery projects using Illumina FASTQ-formatted deep sequencing reads as the input. | https://sourceforge.net/projects/vanator-cvr/ | [155] |
| VirSorter | Predicts prophage and viral sequences in a reference-dependent and -independent manner. Detects circular sequences, performs gene prediction, removes poor quality protein-predicted sequences and those remaining are compared to PFAM and RefSeqABVir or Viromes databases. | https://sourceforge.net/projects/viromescan/ | [156] |
| VirusDetect | Performs virus identification by aligning small RNA reads to a known virus reference database and also performs de novo assembly. | http://virusdetect.feilab.net/cgi-bin/virusdetect/index.cgi | [157] |
| PHASTER | The enhanced release of PHAST for the fast identification and annotation of prophage sequences from assembled metagenomic datasets. | http://phaster.ca | [158] |
| K-mer-based | |||
| MetaVir2 | Web-application interface that works with assembled reads to perform taxonomy assignments based on available sequences in RefSeq. Provides users the option to perform the analysis based on k-mers. | http://metavir-meb.univ-bpclermont.fr | [152] |
| VIP | Developed for identification of viral pathogens from metagenomic datasets. Removes background reads, classifies reads based on nucleotide and amino acid homology, and uses k-mer based de novo assembly for evolutionary studies. | https://github.com/keylabivdc/VIP/blob/master/README.md | [159] |
| VirFinder | K-mer-based tool to identify sequence signatures that distinguish viral sequences from host sequences. | https://github.com/jessieren/VirFinder | [160] |