https://pubmed.ncbi.nlm.nih.gov/33996289/

BELOW ARE MOVE VIRUS IDENTIFICATION TOOLS SHARED BY ROB EDWARDS ON TWITTER

Actively developed

Also generates annotated genome maps of virus sequences

Virus identification in metagenomes, Genome annnotation

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7816666/pdf/veaa100.pdf

Scans contigs for virus hallmark genes, removes flanking host DNA from prophages, makes annotated genome map

https://www.biorxiv.org/content/10.1101/2020.05.06.081778v1

https://bitbucket.org/berkeleylab/checkv/src/master/

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.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8201803/

https://zenodo.org/record/4498884#.Y2Q9sHZBxD8

https://www.biorxiv.org/content/10.1101/558171v1

https://academic.oup.com/bioinformatics/article/37/18/2803/6211156

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

https://www.frontiersin.org/articles/10.3389/fgene.2022.885048/full

https://github.com/HIT-ImmunologyLab/DBSCAN-SWA/.

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

Detection of novel human pathogens from raw short/long reads, contigs, genomes; interpretability toolkit available

https://academic.oup.com/bib/article/22/6/bbab269/6326527

DeePaC plugin for real-time analysis (during Illumina sequencing)

https://academic.oup.com/bib/article-abstract/23/1/bbab385/6374063?redirectedFrom=fulltext

https://arxiv.org/pdf/1806.07810.pdf

https://academic.oup.com/nar/article/50/13/e75/6572362

Dinucleotide Relative Abundance difference

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001193

Distilling and refining annotation of metabolism

https://academic.oup.com/nar/article/48/16/8883/5884738

https://www.nature.com/articles/nprot.2017.063

https://portal.nersc.gov/dna/microbial/prokpubs/EarthVirome_DP/

Viral orthologous groups, de novo annotations using metaproteomics

Concensus viral identification, network-based clustering, metaproteomics

https://academic.oup.com/bioinformatics/article/37/22/4202/6300514

https://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/Zayed_efam_2020.1

efam is an expanded, metaproteome-supported HMM profile database of viral protein families. efam-XC is the eXtremely Conservative version of efam.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5768174/

Detects viral sequences and predicts their abundance by pseudoalignment of reads to a database.

Simulate contact networks, transmission networks, phylogenies, and sequences

https://doi.org/10.1093/bioinformatics/bty921

Simulate contact networks, transmission networks, phylogenies, and sequences

Actively developed

Provides virus taxonomy and functional annotation. Webserver available at: https://nmdc-edge.org/genomad/workflow

RNA viruses from the Global Ocean

https://www.science.org/doi/abs/10.1126/science.abm5847

https://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/ZayedWainainaDominguez-Huerta_RNAevolution_Dec2021

Sequence database, HMM profiles, functional annotations, vOTUs

DNA viruses from the Global Ocean

https://www.cell.com/cell/fulltext/S0092-8674(19)30341-1

https://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/GOV2.0

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7895897/?report=reader

http://ftp.ebi.ac.uk/pub/databases/metagenomics/genome_sets/gut_phage_database/

HMMs and genome organisation models

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0422-7

https://www.sciencedirect.com/science/article/pii/S193131282030456X

https://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/Gregory_and_Zablocki_GVD_Jul2020

https://www.biorxiv.org/content/10.1101/2021.07.21.453177v1

https://www.biorxiv.org/content/10.1101/2022.05.15.492003v2

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899465/

Pipeline designed for taxonomic classification and gene function assignment using genomic and marker databases.

https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01180-4

https://pubmed.ncbi.nlm.nih.gov/27153081/

https://academic.oup.com/bioinformatics/article/38/18/4264/6654586

https://www.biorxiv.org/content/10.1101/2022.07.28.501908v1.abstract

https://www.sciencedirect.com/science/article/pii/S0022283621006458

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/)

Public Health toolkit focused on human viruses

https://academic.oup.com/ve/article/6/2/veaa091/6017186?login=false

https://ieeexplore.ieee.org/document/8983280

https://www.biorxiv.org/content/10.1101/2023.01.12.523725v1

https://www.frontiersin.org/articles/10.3389/fgene.2018.00304/full

https://github.com/LaboratorioBioinformatica/MARVEL

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5042410/

Integrates BLAST hits to multiple phage genomes in a database to identify phage sequences in assembled contigs.

MetaviralSPAdes: assembly of viruses from metagenomic data | Bioinformatics | Oxford Academic

https://github.com/ablab/spades/tree/metaviral_publication

Github links to spades. Metaviralspades is a subcommand of spades

https://academic.oup.com/bioinformatics/article/35/22/4537/5480131

Last update (YYYMMDD)

inferring purifying selection in alternative reading frames

https://academic.oup.com/mbe/article/37/8/2440/5815567

https://peerj.com/articles/14055/

https://academic.oup.com/bioinformatics/article/37/Supplement_1/i25/6319660

tools for predicting and identifying phage in metagenomes and metaviromes

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635311/

https://www.biorxiv.org/content/10.1101/2020.08.09.243022v1

https://doi.org/10.1089/phage.2021.0008

artificial neural network (ANN), support vector machines (SVM)

https://academic.oup.com/bioinformatics/article/35/24/5301/5540317

https://www.mdpi.com/1999-4915/14/6/1329

https://www.nature.com/articles/s41598-017-07910-5

https://www.frontiersin.org/articles/10.3389/fgene.2018.00644/full

There is an API but it submits jobs to their server!

https://www.nature.com/articles/s41467-022-28581-5

https://doi.org/10.1002/adbi.201900108

https://journals.plos.org/ploscompbiol/article/authors?id=10.1371/journal.pcbi.1007845

https://academic.oup.com/bioinformatics/article/35/22/4537/5480131

K-mer read based classification, snakemake workflow

https://www.biorxiv.org/content/10.1101/2022.08.05.502982v1.full

https://pubmed.ncbi.nlm.nih.gov/27141966/

Not available for download. Did not run all genomes on their webserver as they are having issues

https://academic.oup.com/bib/article-abstract/23/1/bbab348/6362109

https://github.com/BioMedicalBigDataMiningLab/PHIAF

https://www.biorxiv.org/content/10.1101/598243v1

This tool (a) asks for root permission, and (b) downloads unknown files from a server in Russia without asking, and (c) downloads an uncompressed file of unknown size!

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439882

https://academic.oup.com/bioinformatics/article/38/5/1447/6460800

https://academic.oup.com/nargab/article/3/3/lqab067/6342220

https://doi.org/10.1093/gigascience/giz066

https://academic.oup.com/nar/article/47/W1/W74/5494712

Not available for download. Did not run all genomes on their webserver as they are having issues

https://academic.oup.com/nar/article/49/22/e128/6374144

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223364

PROPHET requires the no longer supported BLAST legacy application, EMBOSS, and BEDTools. Install does not work (multiple issues posted on GitHub).

https://academic.oup.com/bioinformatics/article/24/6/863/194494