| 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 |
eukaryotichafeZ |
| 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 |
|
|
binningProphage Hunter |
| 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 |
