Viral Bioinformatics Tools

Viral Bioinformatics Tools

Need a #virus or #phage bioinformatics tool? Have a #virus or #phage bioinformatics tool? Check out this sheet and add your new tools.

biology, data, list

Name	Category	Individual, multiple, or virome	Phage, Virus, or Both	Methods	Citation	Google Scholar Link to Cluster Representing the Paper	URL	Last update (YYYMMDD)	Notes	Install from conda	Install from pip	Install from source	Database size if required for download	Dependencies	Runs on a laptop	Runs on a cluster	@

MaGplotR	CRISPR		Virus	CRISPR Screens	https://www.biorxiv.org/content/10.1101/2023.01.12.523725v1		https://github.com/alematia/MaGplotR	20230112

SpacePHARER	CRISPR		Phage	CRISPR Spacer Phage-Host Pair Finder	https://www.biorxiv.org/content/10.1101/2020.05.15.090266v1		https://github.com/soedinglab/spacepharer	20220906

BVBRC	Cyberinfrastructure-supported virus tools		Both 	Website 	http://bvbrc.org		https://bitbucket.org/srouxjgi/iphop	Actively developed		No	No	No 	website

iVirus 2.0	Cyberinfrastructure-supported virus tools		Phage	integrating iVirus apps on CyVerse and KBase	https://www.nature.com/articles/s43705-021-00083-3		CyVerse (http://tinyurl.com/4ndkt4n2), KBase (https://kbase.us/applist/)

DePP	Depolymerase finder		Phage				https://timskvortsov.github.io/WebDePP/

PhageDPO	Depolymerase finder		Phage 	SVM and ANN			bit.ly/phagedpo	2022								Yes

OLGenie	Diversity and selection analysis		Both	Program for estimating dN/dS in overlapping genes (OLGs); inferring purifying selection in alternative reading frames; intrahost; within-host; evolution; selection; nucleotide diversity	https://academic.oup.com/mbe/article/37/8/2440/5815567		https://github.com/chasewnelson/OLGenie	20221202	Perl	No	No	Yes		Perl	Yes	Yes

SNPGenie	Diversity and selection analysis		Both	Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data; intrahost; within-host; evolution; selection; nucleotide diversity	https://academic.oup.com/bioinformatics/article/31/22/3709/241742		https://github.com/chasewnelson/snpgenie	20230822	Perl	Yes	No	Yes		Perl	Yes	Yes

VCFgenie	Diversity and selection analysis		Both	Program for reproducibly filtering VCF files and eliminating false positive variants; intrahost; within-host; evolution; selection; nucleotide diversity	In revision		https://github.com/chasewnelson/VCFgenie	20220825	Python	No	No	Yes		Python libraries argparse, collections, numpy, operator, os, re, scipy, sys, typing, vcf, (pyvcf)	Yes	Yes

VIPERA	Evolutionary analysis		Virus	Phylogenetic and population genetics-based analysis of intra-patient SARS-CoV-2	https://doi.org/10.1101/2023.10.24.561010	https://scholar.google.es/scholar?oi=bibs&hl=en&cluster=7842293868566810584	https://github.com/PathoGenOmics-Lab/VIPERA	20231108		No	No	Yes		Snakemake, Python	Yes	Yes

MetaCerberus	Genome and virome annotation 		Both	HMM-based with Ray MPP	https://doi.org/10.1093/bioinformatics/btae119 		https://github.com/raw-lab/MetaCerberus	2023	Python	Yes	Yes	Yes

DRAMv	Genome annnotation		Phage	Distilling and refining annotation of metabolism	https://academic.oup.com/nar/article/48/16/8883/5884738		https://github.com/WrightonLabCSU/DRAM	2023		Yes	Yes					Yes

PhANNs	Genome annnotation		Phage		https://journals.plos.org/ploscompbiol/article/authors?id=10.1371/journal.pcbi.1007845		PhANNs		Online only   (there is a Python version that can be installed locally - contact Anca Segall, asegall@sdsu.edu)				website		(yes)

Pharokka	Genome annnotation		Phage 		https://doi.org/10.1093/bioinformatics/btac776		https://github.com/gbouras13/pharokka	20230124		Yes		yes

coronaSPAdes	Genome assembly		Both	HMM-synteny guided assembly (works for all viruses)	https://academic.oup.com/bioinformatics/article/38/1/1/6354349		https://github.com/ablab/spades/tree/metaviral_publication

metaviralSPAdes	Genome assembly		Both		MetaviralSPAdes: assembly of viruses from metagenomic data | Bioinformatics | Oxford Academic	https://scholar.google.com/scholar?cluster=3947397301410156503&hl=en&as_sdt=0,5	https://github.com/ablab/spades/tree/metaviral_publication

mulitPHATE	Genome comparison		Phage				https://github.com/carolzhou/multiPhATE

PhageClouds	Genome comparison		Phage 	network graphs	https://doi.org/10.1089/phage.2021.0008								I think this is a website, but its down. Cant find the source code

CheckV	Genome completeness		Both		https://www.biorxiv.org/content/10.1101/2020.05.06.081778v1		https://bitbucket.org/berkeleylab/checkv/src/master/	20220906	Not recommended for prophages: from the FAQ: Q: Can I use CheckV to predict (pro)viruses from whole (meta)genomes? A: Possibly, though this has not been tested.	X	x

viralComplete	Genome completeness		Both				https://github.com/ablab/viralComplete/

viralVerify	Genome completeness		Both				https://github.com/ablab/viralVerify/

BacteriophageHostPrediction	Host prediction		Phage		https://www.nature.com/articles/s41598-021-81063-4	https://scholar.google.com/scholar?cluster=3449135478742512651&hl=en&as_sdt=0,5	https://github.com/dimiboeckaerts/BacteriophageHostPrediction

CHERRY	Host prediction		Phage		https://academic.oup.com/bib/article/23/5/bbac182/6589865	https://scholar.google.com/scholar?cluster=2950777594899421181&hl=en&as_sdt=0,5	https://github.com/KennthShang/CHERRY

CrisprOpenDB	Host prediction		Phage		https://doi.org/10.1093/nar/gkab133	https://scholar.google.com/scholar?cluster=17629824852368187775&hl=en&as_sdt=0,5	https://github.com/edzuf/CrisprOpenDB

DeepHost	Host prediction		Phage 	CNN	https://academic.oup.com/bib/article-abstract/23/1/bbab385/6374063?redirectedFrom=fulltext		https://github.com/deepomicslab/DeepHost	20220804

HostG 	Host prediction		Phage 	GCN	https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01180-4		https://github.com/KennthShang/HostG	20220316

HostPhinder	Host prediction		Phage 	k-mers	https://pubmed.ncbi.nlm.nih.gov/27153081/		https://github.com/julvi/HostPhinder	20200902

INFH-VH	Host prediction		Phage		https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3082-0		https://github.com/liudan111/ILMF-VH

MVP	Host prediction		Both		https://academic.oup.com/nar/article/46/D1/D700/4643372?login=true		http://mvp.medgenius.info/home

PHERI	Host prediction		Phage		PHERI		https://github.com/andynet/pheri

PHIAF 	Host prediction		Phage 	GAN	https://academic.oup.com/bib/article-abstract/23/1/bbab348/6362109		https://github.com/BioMedicalBigDataMiningLab/PHIAF

PHISDetector	Host prediction		Phage				http://www.microbiome-bigdata.com/PHISDetector/index/

PHIST	Host prediction		Phage	k-mers	https://academic.oup.com/bioinformatics/article/38/5/1447/6460800		https://github.com/refresh-bio/phist			No	No	Yes			Yes	Yes

PHP	Host prediction		Phage				https://github.com/congyulu-bioinfo/PHP

PredPHI	Host prediction		Phage				https://github.com/xialab-ahu/PredPHI

RaFaH	Host prediction		Phage		https://www.sciencedirect.com/science/article/pii/S2666389921001008		https://sourceforge.net/projects/rafah/

vHulk	Host prediction		Phage		https://www.biorxiv.org/content/10.1101/2020.12.06.413476v1	https://scholar.google.com/scholar?cluster=11368629964070696550&hl=en&as_sdt=0,5

VIDHOP	Host prediction		Both	Deep learning	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7454304/		https://github.com/flomock/vidhop	20230507		Yes	No	Yes

VirHostMatcher	Host prediction		Phage 	oligonucleotide frequency based distance and dissimilarity measures 	https://pubmed.ncbi.nlm.nih.gov/27899557/		https://github.com/jessieren/VirHostMatcher

VirHostMatcher-Net	Host prediction		Virus		https://academic.oup.com/nargab/article/2/2/lqaa044/5861484?login=true	https://scholar.google.com/scholar?cluster=11117917300880093415&hl=en&as_sdt=0,5	https://github.com/WeiliWw/VirHostMatcher-Net

VirMatcher	Host prediction		Phage 	Leveraging multiple methods and assigning a confidence score	https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(20)30456-X		https://bitbucket.org/MAVERICLab/virmatcher/src/master/	20220429	Leveraging multiple methods (host CRISPR-spacers, integrated prophage, host tRNA genes, and k-mer signatures calculated by WIsH)	Yes				NCBI BLAST, tRNA-Scan SE, MINCED, WIsH	Maybe (linux system)	Yes

Virus Host DB	Host prediction		Both		https://pubmed.ncbi.nlm.nih.gov/26938550/		https://www.genome.jp/virushostdb/

Virus Host Predict	Host prediction		Both				https://github.com/youngfran/virus_host_predict

WIsH	Host prediction		Phage 		https://academic.oup.com/bioinformatics/article/33/19/3113/3964377#:~:text=WIsH%20predicts%20prokaryotic%20hosts%20of,3%20kbp%2Dlong%20phage%20contigs.	https://scholar.google.com/scholar?cluster=10819291780843937718&hl=en&as_sdt=0,5	https://github.com/soedinglab/WIsH

DeePaC	Host prediction 		Both	CNN, ResNet, Shapley values (interpretability)	https://academic.oup.com/nargab/article/3/1/lqab004/6125551, https://academic.oup.com/bib/article/22/6/bbab269/6326527, https://academic.oup.com/bioinformatics/article/38/Supplement_2/ii168/6702016	https://scholar.google.com/scholar?cluster=15260546894544767325&hl=en&as_sdt=0,5	https://gitlab.com/dacs-hpi/deepac	20221216	Detection of novel human pathogens from raw short/long reads, contigs, genomes; interpretability toolkit available	Yes	Yes	Yes		Tensorflow, shap	Yes (GPU recommended)	Yes

DeePaC-Live	Host prediction 		Both	ResNet	https://academic.oup.com/bib/article/22/6/bbab269/6326527		https://gitlab.com/dacs-hpi/deepac-live	20210123	DeePaC plugin for real-time analysis (during Illumina sequencing)	Yes	Yes	Yes		DeePaC, HiLive	Yes (GPU recommended)	Yes

iPHoP	Host prediction 		Phage		https://www.biorxiv.org/content/10.1101/2022.07.28.501908v1.abstract

DRAD	Identify Integrated Viruses		Phage 	Dinucleotide Relative Abundance difference	https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001193		Does not exist any more	None

geNomad