[Verse 1] Shotgun blast through the soup of the microbiome, every genome's a voice in a crowded catacomb, amplicon's narrower, sixteen S is the barcode, DADA2 denoises till the ASV's decoded, Kraken2 chews k-mers, spits back who's in the room, MetaPhlAn counts markers, clocks the species and the bloom, assemble the contigs, then bin with MetaBAT2, CheckM2 grades the draft — completeness, contamination too, watch the kitome creeping, that's the kit's own DNA, blank controls tell truth when the signal drifts away. [Chorus] One reference ain't enough, that's the lesson of the days, Metagenome, Pangenome — mnemonic for the maze, M and P, read the tree, variation's in the graph, sample the whole world before you draw the average. [Verse 2] Old reference genome, single line, one story told, but real humans carry structure that the line can't hold, reference bias hides in every heterozygous site, so we bend the map into a graph and let it hold both sides, Minigraph-Cactus stitches genomes into bubbles, PGGB pours pairwise, builds it through the rubble, vg giraffe glides reads across the haplotype terrain, Human Pangenome Consortium redrew the whole domain, dozens of assemblies, telomere to telomere, every population's variant finally living here. [Verse 3] Microbial fingerprint — MLST types the strain, core genome's the shared chorus, accessory's refrain, Panaroo sorts the pangenome of bacteria in bloom, AMR gene detection flags resistance in the room, outbreak SNP analysis traces who infected who, count the mutations, build the tree, follow the residue, viral consensus calling names the majority base, lineage assignment tags the clade, gives the strain a face, intra-host variation — quasispecies in one host, minor alleles whisper what the average missed the most. [Chorus] One reference ain't enough, that's the lesson of the days, Metagenome, Pangenome — mnemonic for the maze, M and P, read the tree, variation's in the graph, sample the whole world before you draw the average. [Bridge] Cell-free DNA drifting loose in plasma's tide, fragmentomics reads the cut sites, nucleosomes as guide, liquid biopsy catches tumor whispers in the blood, fetal fraction measures placenta in the flood, CRISPR guide design — twenty bases, PAM in sight, score the on-target, score the off, before you cut and splice, CRISPResso2 counts the indels, shows what changed, synthetic biology, DNA storage — data rearranged. [Outro] Metagenome, Pangenome, graph instead of line, every strand's a witness — read the whole design.
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