PhaBOX 2.1.10

Dec 26, 2024

Important

Now, the end-to-end task allow to skip the PhaMer(virus identification).
If users already have the viral contigs as their inputs, they can run end-to-end task using --skip Y to skip the virus identification
However, please noted that the default parameters is --skip N

We also added a log output that tells the user that PhaMer detected no viruses and stopped the following pipelines in the end-to-end task in --skip N condition.

PhaBOX 2.1.9

Dec 9, 2024

Important

Add a new column for the PhaGCN so that bacteriophages can be easily identified now.
Set a more flexible mode for diamond alignments

PhaBOX 2.1.8

Dec 6th, 2024

• Revised some typos in the name of the outputs and Wiki
• Allows more sensitive search during protein alignments
  • This may affect the results.
  • On the benchmark test set, this version improved the recall of the overall performance and the precision will not be affected.

PhaBOX 2.1.7

Nov 27th, 2024

Important

Adjust the default parameters for the phylogenetic task
- marker alignment coverage --mcov: 50
- marker alignment identity --mpident: 25

• Add message information when the calling program (diamond, blast+, fasttree, etc.) fails.

PhaBOX 2.1.6

Nov 21th, 2024

• Revised some typos in the --help descriptions
• Host nodes are added to the cherry's network for better visualization

PhaBOX 2.1.5

Nov 11th, 2024

Version 2.1.5

Updates:

• Fixed a bug that --task tree will incorrectly combine DNA and Protein sequences in one file
• Fixed some typos in the scripts

PhaBOX 2.1.4

Nov 6th, 2024

Version 2.1.4

Updates:

• All the os.system() are replaced by subprocess.run(), providing standard error and return a non-zero exit code in case one of the calls fails.
• Providing a short parameters for --dbdir (-d) and --outpth (-o)

PhaBOX 2.1.3

Nov 4th, 2024

Version 2.1.3

Updates:

• PhaVIP will provide an additional output phavip_prediction.csv. A detailed explanation of this file can be found via PhaVIP outputs
• The protein annotation file gene_annotation.tsv will provide the alignment identity and coverage information as new columns.
• Fixed a potential issue when running phylogenetic tree (FastTree) in the tree task. Users should re-download the PhaBOX v2 database if they would like to run the tree task. Download link
• Fixed a typo in the PhaTYP program.

PhaBOX 2.1.2

Updates:

• End_to_end mode will only make predictions on the predicted viruses. For low-confidence viruses and non-viruses with a flag lower than the viral score threshold, we provide a file named uncertain_sequences_for_contamination_task.fa. We suggest the user run the contamination task to check the quality of their sequences first.
• The contamination task will provide four more fasta files for users: low_quality_virus.fa, medium_quality_virus.fa, high_quality_virus.fa and a cropped proviruses.fa. Users can use them to re-run other tasks.

PhaBOX 2

PhaBOX has now been upgraded to the 2.0 version with faster speed!

There are some major components, including:

🎉 Generalized to all kinds of viruses

🎉 Virus identification

🎉 Taxonomy classification

🎉 Host prediction

🎉 Lifestyle prediction

🎉 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.