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A metapangenome is a way of comparing a bunch of genomes based both on the gene clusters they contain (like in a pangenome) and their abundances in different environments/samples (using metagenomic read recruitment).

Here is a wonderful workflow that takes you through the analysis of 31 Prochlorococcus isolate genomes and 93 TARA Oceans metagenomes, based on this paper.

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