I've seen a few older threads on this, but no real consensus yet. Anyone have a script or method for finding circular DNAs (*osmids, minicircles) in an assembly? I suppose it's really just as "simple" as discovering the motif which is repeated and the beginning and end of the contig where it's circularized. Anyone attempted anything like this yet?
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I looked for plasmids in my assemblies by looking for contigs with the same sequence at both ends. I was able to verify that some of the contigs were plasmids by PCR and sequencing but I was not able to get a product for most of them though I was not very exhaustive in the primers that I tried. While this method works, I don't know that I would trust that you found circular DNA without a second verification.
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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
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