Comments (7)
It was designed for isolate genomes, but I believe it could certainly be adapted for metagenomes! I have tried doing this a bit myself. You'd want to create a good set of reference genomes that represent abundant members of your metagenomic communities, and then it should work pretty well. You may have to alter some settings that assume haploid genomes. I can help you if you get stuck.
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Thank you so much for the quick reply! I have chosen some reference bacterial genome (Facelibacteria)to test whether it can work. It seems that around 5000 insertion sequences were detected in the whole cohort. here you mentioned "You may have to alter some settings that assume haploid genomes. ", could you elaborate on it? Thanks a lot
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Hi Matt
Thank you for the reply! It should be a good idea to lower down the detection threshold and manually check the annotated elements. I will try to see what the result looks like afterward.
I am annotating the elements now and detected some intact prophage which probably shows that the results are reliable in some certain content. For metagenomics detection, I am worried that there are some insertion elements that do not belong to the reference genomes. For example, we detect one insertion termini using Facelibacteria as a reference genome and then assign consensus flanks against the assembly of the whole community (for example, including E. coli). There are possibly some insertion sequences from E. coli or other bacteria other than Faceli (for example). I feel in principle, this case should occur. Do you have idea how to avoid it?
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Hi Matt
I have tested to lower the default parameter as you suggested before which worked very well. Thanks very much. Right now I am thinking about how to set up a threshold to determine that bacteria occur in high frequency or low frequency. Do you have any suggestions about that? In addition, do you have any ideas on how to choose the most suitable reference genome?
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Related Issues (20)
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