Supplementary material for the Paper
"VPF-Class: Taxonomic assignment and host prediction of uncultivated viruses based on viral protein families"

This page contains the supplementary material for the paper

Authors:

• Joan Carles Pons¹
• David Paez_Espino²
• Gabriel Riera¹
• Natalia Ivanova²
• Mercè Llabrés¹
• Nikos C. Kyrpides²

Download

• VPF-Class can be obtained from https://github.com/biocom-uib/vpf-tools
• All the required data files to run it are available as a single compressed file here: vpf-class-data.tar.gz
VPF classification NCBI test Prophages test UViGs test GOV (subset) test Column descriptions
	Baltimore	Family	Genus	Host Domain	Host Family	Host Genus
Summary	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)
Full data	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)
UViG Score samples	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)
	Baltimore	Family	Genus	Host Domain	Host Family	Host Genus
Coverage	(png)	(png)	(png)	(png)	(png)	(png)
Confidence score	(png)	(png)	(png)	(png)	(png)	(png)
Accuracy	(png)	(png)	(png)	(png)	(png)	(png)
Coherence (vConTACT2)	(png)	(png)	(png)	(png)	(png)	(png)
VPF-Class output	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)
Summarized data	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)
	Baltimore	Family	Genus	Host Domain	Host Family	Host Genus
Coverage	(png)	(png)	(png)	(png)	(png)	(png)
Confidence score	(png)	(png)	(png)	(png)	(png)	(png)
Accuracy	N/A	N/A	N/A	(png)	(png)	(png)
Coherence (vConTACT2)	N/A	N/A	N/A	N/A	N/A	N/A
VPF-Class output	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)
Summarized data	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)
	Baltimore	Family	Genus	Host Domain	Host Family	Host Genus
Coverage	(png)	(png)	(png)	(png)	(png)	(png)
Confidence score	(png)	(png)	(png)	(png)	(png)	(png)
Coherence (vConTACT2)	(png)	(png)	(png)	(png)	(png)	(png)
VPF-Class output	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)
Summarized data	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)
	Baltimore	Family	Genus	Host Domain	Host Family	Host Genus
Coverage	(png)	(png)	(png)	(png)	(png)	(png)
Confidence score	(png)	(png)	(png)	(png)	(png)	(png)
Coherence (vConTACT2)	(png)	(png)	(png)	(png)	(png)	(png)
Summarized data	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)	(tsv)
VPF classification (Summary)
This is a summary of the VPF classification at each level.
1. classification: Each considered classification at this level.
2. nvpfs_1.1: Number of VPFs classified at category 1.1.
3. nvpfs_1.2: Number of VPFs classified at category 1.2.
4. nvpfs_1.3: Number of VPFs classified at category 1.3.
5. nvpfs_1.4: Number of VPFs classified at category 1.4.
6. nvpfs_total: Total number of classified VPFs.
7. vpfs: Semicolon-separated list of VPF,membership_ratio,category tuples.
VPF classification (Full data)
These are the required input files that specify the VPF classification.
1. VPF: VPF name/identifier
2. classification: Each considered classification at this level.
3. percentage: Membership ratio of this classification wrt. the VPF.
4. category: Category of this classification wrt. the VPF.
Tests (VPF output)
These are the raw VPF-Class output files for each test.
1. virus_name: Virus identifier from the input FASTA file.
2. class_name: Each possible classification of this virus.
3. membership_ratio: Membership ratio of this classification.
4. virus_hit_score: Total score of this virus (independent of the classification).
5. confidence_score: Confidence score of this virus (independent of the classification).
Tests (Summarized data)
These files contain statistics of our prediction and comparisons to reference classifications and other tools. These are organized as one record for each confidence_score_threshold,membership_ratio_threshold pair and have been used to plot all our heatmaps.
In some cases, some columns may appear with a suffix like _dsDNA or _Eukaryota. These columns have the same meaning as their counterparts without any suffixes, but calculated by restricting the input sequences to viruses under this taxonomic/host classification.
1. confidence_score_threshold: Applied confidence score threshold.
2. membership_ratio_threshold: Applied membership ratio threshold.
3. ncontigs: Number of contigs in the input FASTA file.
4. nclass: Number of different classified viruses.
5. nhomog: Number of different homogenously classified viruses.
6. coverage: nclass over ncontigs.
7. (optional) nclass_known: Number of different classified viruses with a known taxonomy/host.
8. (optional) accuracy_score: The sum of proportions of correct classifications.
9. (optional) nused_clusters: Number of vConTACT clusters that contain at least one pair of viruses classified by VPF-Class.
10. (optional) vc_avg_check_size: Average number of viruses classified by VPF-Class in each considered vConTACT cluster.
11. (optional) vc_avg_coherence: Average vConTACT cluster coherence, where the coherence of a cluster is computed as the proportion of virus pairs with some common VPF-Class classification at this level in that cluster.
12. (optional) vc_cor_coherence: Correlation between cluster check size and coherence.