[Verse 1]
(Male)
BED starts at zero, VCF starts at one,
Same base, different counting, that's how bugs get spun,
Off-by-one error hiding in your interval math,
Convert it wrong once, you erase the whole path.
(Female)
SAM flag's a bitmask, sixteen bits of truth,
Flip it, read it sideways, decode the proof,
CIGAR's the story—match, insert, deletion, skip,
Read the letters like a captain reading the ship.
[Chorus]
(Both)
Fluent when you flag it, fluent when you align it,
Fluent when the coordinates don't leave you behind it,
K-mer, pileup, likelihood, GIAB grade—
Say the acronym, then show me how it's made!
(Female)
Zero-based, half-open—
(Male)
—flip the bit and know it—
(Both)
That's the mnemonic, don't just hum it, show it!
[Verse 2]
(Female)
Smith-Waterman scores a matrix, local not global,
Trace back through the zeros, that's the align you're solvin',
FM-index walks backward, suffix array compressed,
Rank and count in constant time, that's the bug you test.
(Male)
Repeats confuse assembly, tangle up the graph,
Short reads can't span 'em, that's the honest laugh,
Long reads bridge the gap like a rope across the ditch,
Coverage tells the k-mer spectrum which peak's which.
[Verse 3]
(Male)
Genome size from k-mers—find the haploid peak,
Total bases over depth, that's the math you seek,
Pileup gives you counts, ref versus alt allele,
Binomial likelihood tells you what the diploid's real.
(Female)
Ti over Tv near three, that's transition bias true,
FRiP and TSS enrichment, ATAC's checking you,
N50, BUSCO, lambda GC skew—
QC ain't optional, it's the compass pointing true.
[Chorus]
(Both)
Fluent when you flag it, fluent when you align it,
Fluent when the coordinates don't leave you behind it,
K-mer, pileup, likelihood, GIAB grade—
Say the acronym, then show me how it's made!
(Male)
Population stratified—
(Female)
—correct it with PCA and pride—
(Both)
That's the mnemonic, don't just hum it, show it!
[Bridge]
(Female, half-time)
Ancestry skews your GWAS, structure hides in the noise,
Principal components sort the signal from the ploys,
(Male)
Choose your platform for the question—short reads, long reads, depth,
Justify the coverage or your data's got no breath.
(Both, building)
Container it, test it, hand it to a stranger,
Reproducible pipeline—no hidden danger!
[Verse 4]
(Male)
Benchmark your pipeline, run it against truth sets,
Precision, recall, F-score—no room for regrets,
(Female)
Docker or Singularity, snakemake or nextflow,
Someone else should rerun it and get the same info.
[Chorus]
(Both)
Fluent when you flag it, fluent when you align it,
Fluent when the coordinates don't leave you behind it,
K-mer, pileup, likelihood, GIAB grade—
Say the acronym, then show me how it's made!
[Outro]
(Female, fading)
Zero-based, half-open—
(Male)
—the genome don't lie—
(Both)
Prove you're fluent, prove you're fluent, or say goodbye.