Local version of PhaBOX2 web server
This is the source code of our website PhaBOX2, consisting of the latest updates of our previously released programs: PhaMer, PhaGCN, CHERRY/HostG, and PhaTYP.
Please download this local version for large-scale sequencing data and use more threads to speed up the program.
If you like our tool, please give us a star on GitHub. This will provide power for our ongoing maintenance, thanks！
PhaBOX has now been upgraded to the 2.0 version with faster speed!
There are some major components, including:
🎉 Generalized for all kinds of viruses; more than just bacteriophage
🎉 Virus identification (latest PhaMer)
🎉 Taxonomy classification (latest PhaGCN)
🎉 Host prediction (latest CHERRY/HostG)
🎉 Lifestyle prediction (latest PhaTYP)
🎉 Contamination/provirus detection
🎉 vOTU grouping
🎉 Phylogenetic tree based on marker genes
🎉 Viral protein annotation
🎉 All the databases are updated to the latest ICTV 2024 release
If you have any more suggestions, feel free to let me know! We consider long-term maintenance PhaBOX and adding modules according to your needs
You can post an issue or directly email me (jiayushang@cuhk.edu.hk). We welcome any suggestions.
Important
If you are a new user, please check our WIKI page. We provide a tutorial to help you get started quickly and understand how to use PhaBOX2. We hope you will enjoy it!
If you are familiar with the PhaBOX2, please check our Update log. We may have some updates to the program to make it more useful. If you want to use the latest version, please also upgrade your PhaBOX2
To use this version, please also update your phabox database as below:
wget https://github.com/KennthShang/PhaBOX/releases/download/v2/phabox_db_v2_1.zip
Important
New functions were added to the taxonomy classification (--phagcn), host prediction (--cherry), and phylogenetic tree (--tree)
- The taxonomy classification task allows classification of viruses at the species level.
- The Host prediction task allows the user to provide the GTDB-tk taxonomy file (gtdbtk.tsv) for high-confidence filtering and labeling (--bgtdb gtdbtk.tsv).
- The phylogenetic tree task allows running MSA and tree construction without genes from the database (--msadb Y or N).
- A marker_stats.tsv file (information of marker genes in the database) will be copied to the final_prediction folder once the tree task is finished.
Important
New functions were added to the cherry host prediction task We also adjust the host prediction logic as below:
- CRISPRs from MAGs (if MAGs were provided)
- BLASTN (prophage) from MAGs (if MAGs were provided)
- Protein organization compared to the viruses in the database
- Kmer frequency compared to MAGs (if MAGs were provided)
- CRISPRs from the database
New added parameters in --task cherry
--prophage
Minimum alignment length for estimating potential prophage || default: 1000 || range from 0 to 100000
The PhaBOX pipelines are released under the terms of the GPL v3.0 License.