Usage of --cherry --prophage in WGS and update questions

[WUD2018]

Dear Jiayu,

I have two questions of the new version 2.1.11

1. should the WGS data can be used with the --cherry --prophage task? I found it works and give results but how accurate it is? should I trust the results? will the threshold be changed when it comes to WGS (150bp HTS SPAdes-assembled genome) data.

2. I have another version 2.1.9 installed, but in a conda environment. If I update it to v2.1.11, should I use conda or pip as you suggested? like:

git clone https://github.com/KennthShang/PhaBOX.git
cd PhaBOX
python -m pip install . # will this process be installed in base environment? or base python? this is my concern.

Thanks.

D.Wu

[KennthShang]

Hi @WUD2018

If you have the prokaryotic (bacteria or archeara) MAGs, the command should be:

phabox --task cherry -o [output folder] -d [database folder] --contigs [your phage contig] --bfolder [folder of your MAGs]

If you only want to predict phage-MAG connections, you can add --magonly Y. --prophage [length] is an option to decide how long you will consider a prophage, and the default value is an empirical parameter from research papers such as Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome
. BTW, the pipeline will first predict phage-MAG connections by CRISPRs then prophage. If there are no phage-MAG connections and --magonly is not set, it will search for candidate connections from the database.

For the second question, if you have updated to 2.1.11 via bioconda, then it is fine. Otherwise, you do need to run the codes below:

git clone https://github.com/KennthShang/PhaBOX.git
cd PhaBOX
python -m pip install .

Best,
Jiayu

[WUD2018]

Hi @WUD2018

If you have the prokaryotic (bacteria or archeara) MAGs, the command should be:

phabox --task cherry -o [output folder] -d [database folder] --contigs [your phage contig] --bfolder [folder of your MAGs]

If you only want to predict phage-MAG connections, you can add --magonly Y. --prophage [length] is an option to decide how long you will consider a prophage, and the default value is an empirical parameter from research papers such as Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome . BTW, the pipeline will first predict phage-MAG connections by CRISPRs then prophage. If there are no phage-MAG connections and --magonly is not set, it will search for candidate connections from the database.

For the second question, if you have updated to 2.1.11 via bioconda, then it is fine. Otherwise, you do need to run the codes below:

git clone https://github.com/KennthShang/PhaBOX.git
cd PhaBOX
python -m pip install .

Best, Jiayu

Dear Jiayu,

Thanks for your reply. My first question is about how to use it for WGS data, should it be treated the same as MAGs?

[KennthShang]

Sure, you can treat it the same as MAGs (one genome a file).

Best,
Jiayu

[WUD2018]

Sure, you can treat it the same as MAGs (one genome a file).

Best, Jiayu

Thanks, phabox is really getting better and better.

[KennthShang]

Thanks!

If there are further needs in analysis, please let us know. We would like to add them as extensions in future updates.

Best,
Jiayu