Capsid Community

近年、環境ウイルス分野のツールが数多く報告され、ツール選択は非常に困難です。このように類似ツールが群雄割拠している現状は、新規参入の障壁や研究間比較の難化など、分野の大きな問題になっていると考えられます。
Capsid Communityは、このような環境ウイルス分野のツールの情報をまとめ、(今後)比較することで、そのような課題を解決する場になることを目指したコミュニティです。本コミュニティはまだまだ未熟ですが、ぜひ気軽にContributeしていただき、コミュニティ参加者の力によってより使いやすいものにしていければと思います。 Contributeの仕方がわからない場合は、Issueにコメントいただけますと、リストに加えます。カプシドタンパクが自己集合するように、研究に役立つ知識が自己集合するコミュニティとなることを願っています。
(本コミュニティは微生物生態学会の環境ウイルス研究部会( http://www.microbial-ecology.jp/?page_id=7424 )の皆様によって支えられています)
In recent years, a large number of bioinformatics tools have been reported in the field of environmental virology. Thus, the selection of tools for researchers is getting more and more difficult, and it is a high barrier to entering this field for newcomers. The “Capsid Community” aims to be a place where such issues can be resolved by gathering information of the tools and (in the future comparing them). Please feel free to contribute to Capsid Community. If you do not know how to contribute github, please comment on the issue and we will add you to the list. We hope that this community will be a place where knowledge useful for research can self-assemble, just as self-assemby of capsid proteins.
(This community is supported by members of the Environmental Virus Research Group of the Japanese Society of Microbial Ecology)

Tools

ウイルス（ファージ）配列の予測(Prediction of viral and prophage sequences)

Name	Prophage detection	Link	Reference link	Kazumax	Release	Note
VirSorter2	○	https://github.com/jiarong/VirSorter2	https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00990-y	https://kazumaxneo.hatenablog.com/entry/2021/03/07/073000	2021
DeepMicrobeFinder	☓	https://github.com/chengsly/DeepMicrobeFinder	https://www.biorxiv.org/content/10.1101/2021.10.26.466018v1	https://kazumaxneo.hatenablog.com/entry/2021/11/12/080714	2021
VIBRANT	○	https://github.com/AnantharamanLab/VIBRANT	https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00867-0	https://kazumaxneo.hatenablog.com/entry/2020/06/14/175750	2021	AMG prediction
VirSorter	○	https://github.com/simroux/VirSorter	https://peerj.com/articles/985/	https://kazumaxneo.hatenablog.com/entry/2019/01/10/103631	2015
PPR-Meta		https://github.com/zhenchengfang/PPR-Meta	https://academic.oup.com/gigascience/article/8/6/giz066/5521157	https://kazumaxneo.hatenablog.com/entry/2019/10/09/234533	2019
Prophinder	○	http://aclame.ulb.ac.be/prophinder	https://academic.oup.com/bioinformatics/article/24/6/863/194494		2008
Phage_Finder		http://phage-finder.sourceforge.net/	https://academic.oup.com/nar/article/34/20/5839/3100473		2006
PhiSpy	○	https://github.com/linsalrob/PhiSpy	https://academic.oup.com/nar/article/40/16/e126/1027055		2012
PHASTER	○	https://phaster.ca/	https://academic.oup.com/nar/article/44/W1/W16/2499364		2016	PHAST, PHASTER and PHASTESTみたいな論文はあるが実際にはPHASTESTは全くリリースされていない(開発中？)
ProphET	○	https://github.com/jaumlrc/ProphET	https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223364
MARVEL		https://github.com/LaboratorioBioinformatica/MARVEL	https://www.frontiersin.org/articles/10.3389/fgene.2018.00304/full		2018
VIROME		http://virome.dbi.udel.edu/
Metavir 2		http://metavir-meb.univ-bpclermont.fr/	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-76			expired?
VirFinder		https://github.com/jessieren/VirFinder	https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0283-5
VirMiner		https://github.com/TingtZHENG/VirMiner	https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0657-y	https://kazumaxneo.hatenablog.com/entry/2019/06/03/221724
RabbitV		https://github.com/RabbitBio/RabbitUniq	https://academic.oup.com/bioinformatics/article/38/10/2932/6554196	https://kazumaxneo.hatenablog.com/entry/2022/04/30/004538	2022
viralFlye		https://github.com/Dmitry-Antipov/viralFlye	https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02566-x	https://kazumaxneo.hatenablog.com/entry/2022/02/24/234605	2022	ロングリード
fastv		https://github.com/OpenGene/fastv	https://academic.oup.com/bib/article/22/2/924/5917007]	https://kazumaxneo.hatenablog.com/entry/2021/07/10/224445	2021	Not for phages?
CheckV		https://bitbucket.org/berkeleylab/CheckV	https://www.nature.com/articles/s41587-020-00774-7	https://kazumaxneo.hatenablog.com/entry/2020/05/09/073000	2021	quality check
metaviralSPAdes		https://github.com/ablab/spades/tree/metaviral_publication		https://kazumaxneo.hatenablog.com/entry/2020/05/23/235524		viralVerify
ViralRecall		https://github.com/faylward/viralrecall	https://www.mdpi.com/1999-4915/13/2/150		2021	NCLDV
ViBE		https://github.com/DMnBI/ViBE	https://academic.oup.com/bib/article-lookup/doi/10.1093/bib/bbac204		2022	eukaryotic
hafeZ	○	https://github.com/Chrisjrt/hafeZ.	https://www.biorxiv.org/content/10.1101/2021.07.21.453177v1		2021
Phigaro	○	https://github.com/bobeobibo/phigaro	https://academic.oup.com/bioinformatics/article/36/12/3882/5822875		2020
PhageBoost	○	https://github.com/ku-cbd/PhageBoost	https://academic.oup.com/nargab/article/3/1/lqaa109/6066536#222619888		2020
DBSCAN-SWA	○	https://github.com/HIT-ImmunologyLab/DBSCAN-SWA/	https://www.frontiersin.org/articles/10.3389/fgene.2022.885048/full	https://kazumaxneo.hatenablog.com/entry/2020/08/20/230110	2022
DeePhage		https://github.com/shufangwu/DeePhage	https://academic.oup.com/gigascience/article/10/9/giab056/6366926		2021
ViromeScan		http://sourceforge.net/projects/viromescan/	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2446-3		2016
DeepVirFinder		https://github.com/jessieren/DeepVirFinder	https://link.springer.com/article/10.1007/s40484-019-0187-4		2020
vRhyme		https://github.com/AnantharamanLab/vRhyme	https://academic.oup.com/nar/article/50/14/e83/6584432			binning
Prophage Hunter		https://pro-hunter.bgi.com/	https://academic.oup.com/nar/article/47/W1/W74/5494712		2019
MetaPhage		https://github.com/MattiaPandolfoVR/MetaPhage	https://journals.asm.org/doi/10.1128/msystems.00741-22		2022
Deep6		https://github.com/janfelix/Deep6	https://www.biorxiv.org/content/10.1101/2022.09.13.507819v1		2022	Metatranscriptomic Sequences
Phanta		https://github.com/bhattlab/phanta	https://www.biorxiv.org/content/10.1101/2022.08.05.502982v1		2022
ViromeQC		https://github.com/SegataLab/viromeqc	https://www.nature.com/articles/s41587-019-0334-5		2022	Detecting contamination in viromes
PropagAtE	○	https://github.com/AnantharamanLab/PropagAtE	https://journals.asm.org/doi/10.1128/msystems.00084-22		2022	Detecting active prophages
PhageAI		https://github.com/AnantharamanLab/PropagAtE	https://www.biorxiv.org/content/10.1101/2020.07.11.198606v1		2022
BACPHLIP		https://github.com/adamhockenberry/bacphlip	https://peerj.com/articles/11396/		2021
SourceFinder		https://cge.food.dtu.dk/services/SourceFinder/	https://journals.asm.org/doi/10.1128/spectrum.02641-22		2022	Identification of Chromosomal, Plasmid, and Bacteriophage Sequences

ゲノム(遺伝子)アノテーション(Genome/gene annotation tools)

Name	Type	Link	Reference link	Kazumax	Release	Note
DRAM	AMG setection	https://github.com/WrightonLabCSU/DRAM	https://academic.oup.com/nar/article/48/16/8883/5884738	https://kazumaxneo.hatenablog.com/entry/2022/02/10/000615	2020
VIBRANT	AMG prediction	https://github.com/AnantharamanLab/VIBRANT	https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00867-0	https://kazumaxneo.hatenablog.com/entry/2020/06/14/175750	2021
MetaPop	population analysis	https://github.com/metaGmetapop/metapop	https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01231-0	https://kazumaxneo.hatenablog.com/entry/2021/03/04/084538	2022
VIGOR	gene anotation	https://github.com/JCVenterInstitute/VIGOR4	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-451	https://kazumaxneo.hatenablog.com/entry/2020/11/13/225137	2022(latest)	Eukaryotic virus?
VADR	gene anotation	https://github.com/nawrockie/vadr	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3537-3		2020
pharokka	gene anotation	https://github.com/gbouras13/pharokka		https://kazumaxneo.hatenablog.com/entry/2022/07/03/220509		PHANOTATE×PHROGs
PHANOTATE	gene prediction	https://github.com/deprekate/PHANOTATE	https://academic.oup.com/bioinformatics/article/35/22/4537/5480131	https://kazumaxneo.hatenablog.com/entry/2019/05/30/073000
MetaPhage	gene anotation	https://github.com/MattiaPandolfoVR/MetaPhage	https://www.biorxiv.org/content/10.1101/2022.04.17.488583v1	https://kazumaxneo.hatenablog.com/entry/2022/04/23/124539
VirionFinder	virion proteins identification	https://github.com/zhenchengfang/VirionFinder	https://www.frontiersin.org/articles/10.3389/fmicb.2021.615711/full		2021

配列のClassification (系統分類) Taxonomic classification of viral sequences

Name	Link	Reference link	Kazumax	Release
Vcontact2	https://bitbucket.org/MAVERICLab/vcontact2/wiki/Home	https://www.nature.com/articles/s41587-019-0100-8	https://kazumaxneo.hatenablog.com/entry/2019/09/21/235859	2019
ViPTree	https://www.genome.jp/viptree/	https://academic.oup.com/bioinformatics/article/33/15/2379/3096426		2017
VICTOR	https://ggdc.dsmz.de/victor.php		https://academic.oup.com/bioinformatics/article/33/21/3396/3933260	2017
VIRIDIC	http://rhea.icbm.uni-oldenburg.de/VIRIDIC/	https://www.mdpi.com/1999-4915/12/11/1268		2020
VirClust	http://rhea.icbm.uni-oldenburg.de/virclust/	https://www.biorxiv.org/content/10.1101/2021.06.14.448304v1		2021
GRAViTy	http://gravity.cvr.gla.ac.uk/	https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0422-7		2018
viruses_classifier	https://github.com/wojciech-galan/viruses_classifier	https://www.nature.com/articles/s41598-019-39847-2	https://kazumaxneo.hatenablog.com/entry/2019/03/15/073000	2019
VPF-Class	https://github.com/biocom-uib/vpf-tools	https://academic.oup.com/bioinformatics/article/37/13/1805/6104829		2021
Classiphage	http://appmibio.uni-goettingen.de/index.php?sec=sw	https://www.mdpi.com/1999-4915/11/2/195
VIRify	https://github.com/EBI-Metagenomics/emg-viral-pipelinee
ClassiPhages 2.0	http://appmibio.uni-goettingen.de/index.php?sec=sw	https://www.biorxiv.org/content/10.1101/558171v1
PhageClouds	https://phageclouds.ku.dk/	https://www.liebertpub.com/doi/full/10.1089/phage.2021.0008

宿主予測 Host prediction

Name	Link	Reference link	Kazumax	Release
iPHoP	https://bitbucket.org/srouxjgi/iphop/src/main/	https://www.biorxiv.org/content/10.1101/2022.07.28.501908v1		2022
WIsH	https://github.com/soedinglab/wish	https://academic.oup.com/bioinformatics/article/33/19/3113/3964377		2017
SpacePHARER	https://github.com/soedinglab/spacepharer	https://academic.oup.com/bioinformatics/article/37/19/3364/6207963		2021
VirHostMatcher-Net	https://github.com/WeiliWw/VirHostMatcher-Net	https://academic.oup.com/nargab/article/2/2/lqaa044/5861484		2020
CHERRY	https://github.com/KennthShang/CHERRY	https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbac182/6589865		2022
RaFAH	https://sourceforge.net/projects/rafah/	https://www.biorxiv.org/content/10.1101/2020.09.25.313155v1
HostPhinder	https://cge.cbs.dtu.dk/services/HostPhinder/	https://www.mdpi.com/1999-4915/8/5/116	https://kazumaxneo.hatenablog.com/entry/2018/08/31/164441
PHISDetector	https://github.com/HIT-ImmunologyLab/PHISDetector	https://www.sciencedirect.com/science/article/pii/S1672022922000171		2022
vHULK	https://github.com/LaboratorioBioinformatica/vHULK	https://www.biorxiv.org/content/10.1101/2020.12.06.413476v1
ILMF-VH	https://github.com/liudan111/ILMF-VH	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3082-0
PHISDetector	http://www.microbiome-bigdata.com/PHISDetector/	https://www.biorxiv.org/content/10.1101/661074v2
Host Taxon Predictor (HTP)	https://github.com/wojciech-galan/viruses_classifier	https://www.nature.com/articles/s41598-019-39847-2
ContigNet	https://github.com/tianqitang1/ContigNet	https://academic.oup.com/bioinformatics/article/38/Supplement_1/i45/6617519

CRISPR同定 Identification of host CRISPR sequces

Name	Link	Reference link	Kazumax	Release
CRISPRDetect	http://crispr.otago.ac.nz/CRISPRDetect/predict_crispr_array.html	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2627-0	https://kazumaxneo.hatenablog.com/entry/2019/12/15/130706	2016
MinCED	https://github.com/ctSkennerton/minced
CRISPR Recognition Tool(CRT)	http://www.room220.com/crt/	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-209		2007
crass	https://github.com/ctskennerton/Crass
CRISPRCasFinder	https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index
CRISPRCasTyper	https://crisprcastyper.crispr.dk/	https://www.liebertpub.com/doi/10.1089/crispr.2020.0059
AcrFinder	https://bcb.unl.edu/AcrFinder/	https://academic.oup.com/nar/article/48/W1/W358/5836766		2020
SpacePHARER	https://github.com/soedinglab/spacepharer	https://academic.oup.com/bioinformatics/article/37/19/3364/6207963		2021
CRT	http://www.room220.com/crt//	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-209		2007
PILER-CR	http://www.drive5.com/pilercr.	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-18		2007
CRISPRleader	https://github.com/BackofenLab/CRISPRleader	https://doi.org/10.1093/bioinformatics/btw454		2016

データベース Databases related to virology

Name	Type	Link	Reference link	Release	Note
PHROG	Orthologue db	https://phrogs.lmge.uca.fr/	https://academic.oup.com/nargab/article/3/3/lqab067/6342220	2021	MMseqs2/hhblits search
pVOGs	Orthologue db	http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads.html	https://academic.oup.com/nar/article/45/D1/D491/2333930	2016	Link expired?
Virus-Host DB	Host / Genomes	https://www.genome.jp/virushostdb/	https://www.mdpi.com/1999-4915/8/3/66	2022
ICTV	Taxonomy	https://ictv.global/taxonomy	https://academic.oup.com/nar/article/46/D1/D708/4508876	2021(initial 2018)
IMG/VR	Genomes	https://img.jgi.doe.gov/vr	https://academic.oup.com/nar/article/49/D1/D764/5952208	2021
IVirus	pipeline/tools	https://www.ivirus.us/	https://www.nature.com/articles/s43705-021-00083-3	2021	ver2
VirHostNet	virus/host molecular interactions	https://virhostnet.prabi.fr/	https://academic.oup.com/nar/article/43/D1/D583/2437900	2022	ver3
CRISPRCasdb	CRISPR cas	https://crisprcas.i2bc.paris-saclay.fr/	https://academic.oup.com/nar/article/48/D1/D535/5590637	2019
CrisprOpenDB	CRISPR cas	https://github.com/edzuf/CrisprOpenDB	https://academic.oup.com/nar/article/49/6/3127/6157093#233788514	2021
inphared	Genomes	https://github.com/RyanCook94/inphared)	https://www.liebertpub.com/doi/10.1089/phage.2021.0007	2021
VOG db	Orthologue db	https://vogdb.org/
VPFs	Orthologue db	https://portal.nersc.gov/dna/microbial/prokpubs/EarthVirome_DP/	https://www.nature.com/articles/nprot.2017.063
efam	Orthologue db	https://datacommons.cyverse.org/browse/iplant/home/shared/commons_repo/curated/Zayed_efam_2020.1	https://academic.oup.com/bioinformatics/article/37/22/4202/6300514#312931372
ViPhOGs	Orthologue db	https://osf.io/2zd9r/	https://www.mdpi.com/1999-4915/13/6/1164

プラスミド様配列の検出 Plasmid detection

Name	Link	Reference link	Kazumax(for Japanese beginner)	Release
RFplasmid	https://github.com/aldertzomer/RFPlasmid	https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000683	https://kazumaxneo.hatenablog.com/entry/2020/09/29/233000	2021
PlasFlow	https://github.com/smaegol/PlasFlow	https://academic.oup.com/nar/article/46/6/e35/4807335	https://kazumaxneo.hatenablog.com/entry/2019/05/11/073000	2018
PlassClass	https://github.com/Shamir-Lab/PlasClass	https://academic.oup.com/nar/article/46/6/e35/4807335	https://kazumaxneo.hatenablog.com/entry/2019/10/21/073000	2020
metaplasmidSPAdes	https://github.com/ablab/spades/releases	https://genome.cshlp.org/content/29/6/961.long	https://kazumaxneo.hatenablog.com/entry/2019/06/05/073000	2019
PlasmidSeeker	https://github.com/bioinfo-ut/PlasmidSeeker	https://peerj.com/articles/4588/	https://kazumaxneo.hatenablog.com/entry/2018/05/28/203726	2018
Recycler	https://github.com/Shamir-Lab/Recycler	https://academic.oup.com/bioinformatics/article/33/4/475/2623362	https://kazumaxneo.hatenablog.com/entry/2017/08/27/233654	2018

banhbio/Capsid_community