Virus Prediction with My Bacterial Sequences

KennthShang / HostG

Graph convolutional neural network for host prediction

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Virus Prediction with My Bacterial Sequences #4

Closed drob2727 closed 2 years ago

drob2727 commented 2 years ago

Is it possible to predict the hosts with my own bacterial sequences so I can see which contig belongs to which prediction?

KennthShang commented 2 years ago

Yes, of course. please follow the guidelines ”database extension" to add your data

drob2727 commented 2 years ago

When adding your own bacterial sequences do you have any suggestions on completion and contamination of the genome? For example could I have 5% contamination? I'm currently using 0% and I'm just curious.

KennthShang commented 2 years ago

Ummmm, Since I am a CS student, I am not really sure what is the meaning of contamination. Do you mean your genomes are assembled from metagenomic data and you do not know whether they are pure bacterial contigs? If so, I think the model can still give a prediction, as long as you tell the model they are bacterial contigs.

Best, Jiayu