Is there a tool that can be ran locally for finding phage related sequences in bacterial genomes? I have tried Phage_finder which gave no errors but also no results and ProphET which is proving difficult to install correctly due to its number of dependencies. Thanks
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There are many out there.
A guy I know put together a comparison: https://nickp60.github.io/weird_one_offs/testing_3_prophage_finders/
Note, not all of these are local only (PHASTER for example, is one of the better ones, but you have to interact with their web service via API).
You might be interested in VirSorter and Phigaro.
According to me, you don't need any specific software for finding phage sequence in your data, rather you can just blastn your total sequences against NCBI's NT database or some phage genome database. Sequences showing hit against database phage sequence can then be used for gene prediction followed by its annotation to check for presence of phage essential genes.
I want to be able to run everything locally though that is why I didn't choose that option.
But here also, you will be able to do everything locally. You can download NCBI's NT database and can install standalone blast in your system. For gene prediction, you can use prodigal or glimmer which again can be installed in your local PC followed by blastx against NR database for gene annotation.
you can also go through this publication to get better idea of other tools (online or standalone) which you can use for phage genome analysis.
Thanks for your help, I'll try that out.
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