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biologger / speciesprimer

The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.
GNU General Public License v3.0
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Design primers for viruses #2

Open aiqubo opened 4 years ago

aiqubo commented 4 years ago

I tested speciesprimer and wet the experiment to verify a few bacteria, which did very well. Thank you for your great program! I want to use it in viruses primer design How do I use the SpeciesPrimer pipeline to design primers for viruses?

biologger commented 4 years ago

Thanks for your feedback!

In Theory I would download the virus genomes, annotate them with Prokka and copy the fna, ffn and gff files in the corresponding directories. I actually never tested it but it could work for some cases. However, I plan to implement primerdesign for viruses in a future release.

aiqubo commented 4 years ago

That would be great. I look forward to your update, I really appreciate your assistance

jxshi commented 3 years ago

Hi,

I learned on the Docker SpeciesPrimer mainpage that SpeciesPrimer v2.2 will support primer design for viruses. But I don't know where to get the latest docker file. I pulled the docker file with the following command docker pull biologger/speciesprimer. But speciesprimer.py -V command returned SpeciesPrimer 2.1.2.

    New functions (Beta)
        Strainprimer: strain specific primer design
        Primer design for viruses

Thank you for your awesome pipeline and Happy New Year! Best, Jianxiang

biologger commented 3 years ago

Hi,

Yes, this (experimental) feature is planned, but unfortunately I could not finish the release of version 2.2 due to other projects. A draft for the primer design for viruses is included in the beta version.

$ sudo docker pull biologger/speciesprimer:v2.2-beta.4

However, there is no quality control of input genomes and this version has still some bugs. Also, I have observed problems with the virus names/taxonomy since it was originally designed for bacteria with a stable genus-species scheme. Further, the default settings are optimized for bacterial species. The new nuc_identity threshold may be helpful to get more target sequences for primer design.

I will continue the development as soon I find some time, however it may take a few months.

Best, Matt

jxshi commented 3 years ago

Hi Matt,

Thank you very much for your timely reply and instructions.

I will try to see if I can make it work.

With all my best wishes, Jianxiang