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Smash and grab

I’ve been trying to get my head around next-generation genome sequencing. How it has revolutionised our understanding of microbiomes. From what I can work out, somewhat similar to the arrival of photography early in the 19th century: a fresh way of seeing the world, one that was almost instantaneous, capturing moments and movements as never before. So how does it work? Well, take a sample of (for example) pond water that might contained many hundreds (if not thousands) of bacterial species. Dissolve away the cellular structures and then extract the genetic material. You then ‘smash this around a bit’, breaking the DNA into short segments, before reading the nucleotide sequence of this ragbag of segments. All good so far, except that you are now in the position of trying to separate out the pieces of many very similar jigsaws that have got mixed together in a single box. That is when you put the computer to work analysing these short sequences looking for unique sections, overlaps, repetitions from which it is possible to reconstruct parts of the complete genomes. Finally, by comparing these sequences to examples already present in online databases you can identify the species in your original sample and how homogenous or varied a community of bacteria you actually started out with. That is what this covid infographic is based on, offering the chance to see, almost in real time, how the virus has travelled around the world mutating as it goes. But there is something in this smash-and-grab process that I like. A microbiomic snapshot of sorts. Could it be used to picture a network? Hmmmm…… [Many thanks Jamie for such a fascinating ramble around your world of bioinformatics. So when the history books come to be written, who will be the Fox Talbot of genome sequencing? Image from nextstrain.org]

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