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kantorlab / hivmmer

Alignment and variant-calling pipeline for Illumina HIV sequences.
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Reference enquiry #12

Open nadine-zakkak opened 4 years ago

nadine-zakkak commented 4 years ago

I downloaded the docker version for hivmmer and I noticed that the latest docker version is 0.1.2, will the latest version (0.2.0) be on docker anytime soon?

Also, I noticed that I should be building my own profile Hidden Markov Model but I am unable to figure out how to do so using hivmmer. I tried building a pHMM file for a multiple sequence alignment amino acid sequences using hmmer but it is not working either, it is only working for DNA sequences.

I also read that you have some prepackaged profile Hidden Markov Models for the pol region in version 0.1.2, how can I use them?

mhowison commented 4 years ago

Hi @nadine-zakkak I've released a 0.2.0 version of the Docker image. This includes the pre-packaged profile HMMs for the entire HIV genome, and you should be able to use it without creating your own profiles HMMs. Let me know how it goes!