DNA for Computational Biologists: A Complete Curriculum
Subject: DNA for Computational Biologists: A Complete Curriculum
21 chapters
1. How to Use This Curriculum
[Verse 1]
Set the metronome slow, twenty-four to thirty weeks,
Eight to ten hours, steady river, never leaks,
Modules one through four are bedrock, concrete pour,
Don't skip the footing, biologist or code explorer.
Bio-first, you came from petri dish and pipette,
Linger longer on three and four, don't forget the alphabet,
Appendix A's your friend, it decodes the stats and scripts,
So the terminal window never feels like it bites.
[Chorus]
A-T-C-G, but the syllabus reads different letters,
One through four is the spine, then you pick what's better,
Five to twelve are movable joints, bend them to your question,
Fourteen's the capstone gluing every lesson.
Base by base, week by week, we're building up the strand,
Curriculum's a double helix, easy in your hand.
[Verse 2]
CS-first, you came from clusters, functions, loops that run,
Extra hours in Module one and two before you're done,
Appendix B is waiting with the vectors dense and keen,
Turning noisy k-mers into counts that stay clean,
But don't you dare breeze past the wet-lab chapters, friend,
Three and four explain why every signal has an end,
Because a chromosome's not just a string you can invert,
It's twisted, capped, and histone-wrapped — biologically alert.
[Chorus]
A-T-C-G, but the syllabus reads different letters,
One through four is the spine, then you pick what's better,
Five to twelve are movable joints, bend them to your question,
Fourteen's the capstone gluing every lesson.
Base by base, week by week, we're building up the strand,
Curriculum's a double helix, easy in your hand.
[Verse 3]
Minimum ticket in: Python or R, don't need both yet,
Algebra and a coin flip's odds, that's your safety net,
Hypothesis tests, descriptive stats, high-school gene review,
A terminal you can drive — that's the minimum for you.
Ideal ticket adds some Bash, some Linux breathing room,
Calculus, linear algebra, Bayesian bloom,
GLMs and multiple testing, Git to track your past,
HPC and cloud for when your dataset's too vast.
[Bridge]
Modules five through twelve, they're not one straight line drawn,
Reshuffle like a card deck till your research finds its dawn,
Assembly first, or variants first — the order's only yours,
Just don't you dare walk past the doors marked one through four.
[Verse 4]
Fourteen weeks deep or thirty, however long it took,
The capstone's waiting, end to end, to close the whole book,
Raw reads walk in, a variant report walks out the door,
That's the proof you built the engine, base pair to the core.
[Chorus]
A-T-C-G, but the syllabus reads different letters,
One through four is the spine, then you pick what's better,
Five to twelve are movable joints, bend them to your question,
Fourteen's the capstone gluing every lesson.
Base by base, week by week, we're building up the strand,
Curriculum's a double helix, easy in your hand.
[Outro]
A-T-C-G, remember different letters,
Foundation, flex, and capstone — leave this curriculum better.
2. Module 0 — Computational Environment Setup (Week 0)
[Verse 1]
Terminal glowing, cursor blinking like a pulse on the wall,
Navigate the tree with cd, ls tells you all,
Pipe the output, one command feeding to the next,
Redirect with the arrow, save your echo to a text,
Grep hunts patterns like a hawk through a gene,
Awk slices columns, sed rewrites the scene,
Sort your data, uniq collapses what repeats,
Cut the fields you need, join two files by their seats,
Xargs takes a list and runs it argument by argument,
Parallel spins it wide, ten jobs concurrent —
this is the muscle memory, the fingers learning fast,
build it once, script it right, make the shortcut last.
[Chorus]
Pipe it, grep it, sort it, cut it — conda locks the version, nothing's gutted,
Docker packs it, Apptainer ships it to the cluster,
Git remembers every step so your work don't lose its luster,
Reproduce it, reproduce it, that's the whole refrain,
Same environment forever, no more version-drift pain.
[Verse 2]
Mamba's faster conda, same recipe, less wait,
Bioconda's the pantry where the tools all congregate,
Samtools, bcftools, bedtools, seqkit, Biopython too,
Export it to a YAML, that's your blueprint coming through,
Python venv keeps your snake in its own little pen,
Renv does the same for R, locks packages again,
Now Docker builds a box that runs the same on any host,
Apptainer's the HPC cousin, singular, the shared-cluster ghost —
no root access needed, sandboxed and it's sealed,
what worked on your laptop works out in the field.
[Verse 3]
Git tracks the changes, commit like a diary entry,
Push it up to GitHub, let the README be the sentry,
Explain what the repo does, how to run it, why it's there,
Branch it, merge it, never lose a single edit to despair,
SLURM's the scheduler, sbatch throws your job in queue,
Nodes and cores and walltime, the cluster's point of view,
Cloud storage holds your terabytes of reads,
Compute spins up on demand for whatever the task needs.
[Verse 4]
Jupyter's a notebook, code and prose combined,
Quarto renders documents, tidy and refined,
But scripts are the workhorse, reliable, repeat,
Workflows chain it all together, Snakemake or Nextflow complete,
Choose the tool that fits the job, not the trend of the day,
Document every choice so the future you can replay.
[Bridge]
Zcat the fastq, pipe it into word dash l,
Divide the count by four, that's your read total tell,
One-liners like haiku, small but full of might,
Environment dot yaml, your contract signed and tight.
[Chorus]
Pipe it, grep it, sort it, cut it — conda locks the version, nothing's gutted,
Docker packs it, Apptainer ships it to the cluster,
Git remembers every step so your work don't lose its luster,
Reproduce it, reproduce it, that's the whole refrain,
Same environment forever, no more version-drift pain.
[Outro]
Log it, tag it, commit and push,
Week zero closes, no more rush,
The environment's built, the README's true,
Module one is waiting — the genome's calling you.
3. Module 1 — The DNA Molecule (Weeks 1–2)
[Verse 1]
Deoxyribose spine, a backbone link between,
Adenine, Cytosine, Guanine, Thymine — the coded scene,
Purines are the double rings, A and G stand wide,
Pyrimidines, C and T, single rings collide,
Sugar-acid bonds stitch the ladder tight,
Five prime to three prime, we're reading left to right,
But the partner strand runs backwards, antiparallel design,
Two roads facing traffic, tangled up in twine.
[Chorus]
Zucker, Rückgrat, und die Basen vier,
A findet T, zwei Brücken halten hier,
G und C, drei Brücken, fester Bund,
Doppelhelix dreht sich — komm, wir tanzen im Grund.
Stacking is the muscle, bonds just steady the frame,
Antiparallel lovers who never share a name.
[Verse 2]
Watson-Crick pairing, geometry so precise,
Two bonds for A-T, that's the cheaper price,
Three bonds lock G-C, harder grip to break,
But it's the stacking bases doing heavy lifting for the stake,
B-DNA's the classic, wide and gently curled,
A-form tightens up when the water's pearled,
Z-DNA zigzags left when purines alternate —
Structure isn't fixed, it's a conversation with its state.
[Chorus]
Zucker, Rückgrat, und die Basen vier,
A findet T, zwei Brücken halten hier,
G und C, drei Brücken, fester Bund,
Doppelhelix dreht sich — komm, wir tanzen im Grund.
[Verse 3]
Four G-tracts fold into a quadruplex knot,
Regex hunts them, G three plus in every slot,
Hairpins fold on cruciforms, triplex adds a third,
R-loops let RNA squat where the duplex once occurred,
i-motifs love the acid, C-runs curling tight,
Melting temp depends on how the letters bite —
Wallace rule's a shortcut, nearest-neighbor's the truth,
Supercoils get loosened by topoisomerase, forsooth.
[Verse 4]
5-methyl-C, 6mA, marks written in the code,
8-oxo-G's the damage when oxygen corrodes,
Deamination turns a C into a ghostly U,
UV welds two thymines — that dimer's overdue,
Ancient bones leak C to T where the strand end frays,
Single-stranded overhangs betray their broken days,
Sense or antisense, template, coding, plus or minus track,
Complement it, flip it, N and R and Y ride shotgun on the map.
[Bridge]
Kein Zufall — jede Base hat ihren Platz,
Reverse complement, ich lese dich im Satz,
Skew zeigt mir den Ursprung, wo die Kurven sich drehen,
Ori versteckt im G minus C — ich kann's schon sehen.
[Chorus]
Zucker, Rückgrat, und die Basen vier,
A findet T, zwei Brücken halten hier,
G und C, drei Brücken, fester Bund,
Doppelhelix dreht sich — komm, wir tanzen im Grund.
Stacking is the muscle, bonds just steady the frame,
Antiparallel lovers who never share a name.
[Outro]
Fünf zu drei, drei zu fünf, gegenläufig, treu,
Read the ladder closely — the code was always new.
4. Module 2 — Genome Biology & Organization (Weeks 3–4)
[Verse 1]
Prokaryote's a single loop, no nuclear wall,
eukaryote's chromatin locked inside its hall.
Mitochondria whisper, chloroplast still hum,
old symbionts turned engines, powerhouse and photon drum.
Plasmids ride like hitchhikers, extra rings of gain,
viral genomes cheat the game — DNA or RNA strain,
retrovirus, phage, both playing loaded dice,
capsid to genome ratio — pack it once, pack it twice.
[Chorus]
Genoma é camada, palimpsest escrito e reescrito —
layer under layer, old text never fully deleted.
From the promoter to the polyA, seis quadros, sem parar
Central dogma, minha bússola — DNA, RNA, proteína, vem cá
[Verse 2]
C-value paradox — genome size lies to your face,
an onion's got more base pairs than the human race.
Ploidy's the headcount, karyotype's the photo,
centromere's the waistline, telomere's the coda,
X and Y share borders — pseudoautosomal ground,
recombining at the edges where the sex chromosomes bound.
Satellite repeats coil tight around the centromere,
telomeres shorten quiet every time you replicate, my dear.
[Chorus]
Genoma é camada, palimpsest escrito e reescrito —
layer under layer, old text never fully deleted.
From the promoter to the polyA, seis quadros, sem parar
Central dogma, minha bússola — DNA, RNA, proteína, vem cá
[Verse 3]
Promoter calls the meeting, TSS strikes the gong,
five prime UTR hums the intro to the song,
exons hold the verses, introns get spliced away,
CDS writes the message, polyA signal says okay.
Codons read in triplets, one frameshift wrecks the read,
ATG opens doors, a stop codon plants the seed —
TAA, TAG, TGA, unless the code's rewired,
mitochondrial tables swap the rules that you required.
Operons in bacteria — one promoter, many genes,
codon bias whispers which transcripts run the machines.
[Bridge]
Enhancers shout from far, silencers keep it low,
insulators raise the walls so signals can't cross-flow.
tRNA, rRNA, miRNA trim the fat,
lncRNA and pseudogenes — echoes of what genes once were.
Alu jumps, LINEs stroll, LTRs pack a punch,
nucleosomes spool the thread, histones hold it close,
heterochromatin's silent, euchromatin's loud and open,
loops fold into TADs — compartments A and B,
genome's origami, sculpture in 3D.
[Verse 4]
Six-frame translation — check every starting gate,
ORF finder scans the codons till a stop, then weigh the freight.
GFF3 gives coordinates, exon count and CDS sum,
soft-masked lowercase letters, hard-masked N's struck dumb.
Compare the codon usage in E. coli, fast and slow —
highs pick their favorites, the lows just let the bias go.
Central dogma's got exceptions — reverse transcribe, edit RNA,
splice it, prion-fold it — biologia sempre nos surpreende.
[Chorus]
Genoma é camada, palimpsest escrito e reescrito —
layer under layer, old text never fully deleted.
From the promoter to the polyA, seis quadros, sem parar
Central dogma, minha bússola — DNA, RNA, proteína, vem cá
5. Module 3 — DNA Replication, Repair, Recombination & Mutation (Weeks 5–6)
[Verse 1]
Origin fires, helicase splits the ladder wide,
Two forks racing outward, one continuous, one denied—
Leading strand sprints solo, polymerase glued tight,
Lagging strand stutters, Okazaki fragments, primer, bite.
Fidelity's the watchword, one error in a billion base,
Proofreading domain reads back, kicks the wrong bond off its place,
Replication timing marks the early and the late,
Heterochromatin dozes while the euchromatin can't wait.
[Chorus]
Mismatch, base, nucleotide — three repair crews on patrol,
Cut the wound, fill the gap, ligase seals the scroll,
HR borrows a sister, NHEJ just glues the ends,
Watch the fork, guard the code, that's how the genome defends.
[Verse 2]
Mismatch repair spots the loop the polymerase missed,
Base excision plucks a damaged letter off the list,
Nucleotide excision cuts a patch when UV bends the strand,
Double-strand breaks call for backup, pick a repair band—
Homologous recombination's careful, copies from a template true,
NHEJ's the reckless medic, stitching blunt ends fast, askew,
MMEJ's the shortcut cousin, microhomology as its guide,
Every choice in that decision shapes what mutations will hide.
[Verse 3]
Meiosis shuffles chromosomes, crossovers cut and swap,
PRDM9 marks the hotspots where the recombining won't stop,
Gene conversion copies one allele to overwrite the other—
Non-reciprocal theft between a chromosome and its brother.
Transitions keep it in the family, purine to purine stays,
Transversions cross the aisle, purine turns to pyrimidine ways,
Indels slip like loose scaffolding, MNVs travel in a pack,
Aneuploidy's the whole chromosome that never got sent back.
[Bridge]
CpG's a hot seat, methylate then deaminate to T,
Every cancer genome's a palimpsest — old scratches under new debris,
Layers of signatures written, erased, rewritten again,
Somatic in the tumor, germline passed to kin,
Mosaic cells whisper different codes beneath one skin,
Clonal hematopoiesis — blood's rebellion from within.
[Verse 4]
Count your transitions, count your transversions, divide and you'll see—
Two-point-oh to two-point-one is the genome's steady decree,
Exomes climb to three 'cause CpG islands hide in exons tight,
Build the ninety-six-channel spectrum, trinucleotide left and right,
Simulate the SNVs, dial the Ti/Tv rate you need,
Elevate the CpG channel, watch the signature succeed,
Decompose it with least squares, match it to the known,
Every mutation's a fingerprint — the cell's confession, carved in stone.
[Chorus]
Mismatch, base, nucleotide — three repair crews on patrol,
Cut the wound, fill the gap, ligase seals the scroll,
HR borrows a sister, NHEJ just glues the ends,
Watch the fork, guard the code, that's how the genome defends.
[Outro]
Fork to fix, break to bind, every base earns its stripe,
Read the spectrum, trust the ratio, decode the genotype.
6. Module 4 — Laboratory Methods & How DNA Data Is Generated (Weeks 7–8)
[Verse 1]
Sonicate the strands, shear 'em down to size,
tagmentation's quicker, enzyme cuts and ties,
size selection combs the beads through the mess,
short fragments wander off, long ones pass the test.
PCR fires up, primers find their mark,
denature, anneal, extend — cycling in the dark,
polymerase stumbles, drops a wrong base in,
GC-rich regions starve while AT wins,
duplicates pile up from the same template ghost,
chimeras splice two strangers into one host.
[Chorus]
Extract it, fragment it, amp it, then you read it,
every artifact's a clue if you know how to read it,
adapters, indexes, barcodes on parade,
watch for index hopping when the pools cascade,
cut it, tag it, call it — trust but verify,
Sanger in the corner keeping short reads honest, why.
[Verse 2]
Library prep stitches adapters on the ends,
UMIs are molecular tags, your truest friends,
multiplex a hundred samples in one lane,
but leaky index hopping mixes up the chain,
hybrid capture baits your exons out the crowd,
amplicon panels shout their target loud,
Sanger's the old sage, slow but never lies,
four-color ladder, capillary-sized,
gold standard validation when your caller's unsure,
run it through the Sanger, settle the score.
[Chorus]
Extract it, fragment it, amp it, then you read it,
every artifact's a clue if you know how to read it,
adapters, indexes, barcodes on parade,
watch for index hopping when the pools cascade,
cut it, tag it, call it — trust but verify,
Sanger in the corner keeping short reads honest, why.
[Verse 3]
Illumina clusters glow in cycles of light,
paired-end reads shake hands across the insert's flight,
phasing and pre-phasing blur the tail-end call,
quality decays like a whisper down the hall,
patterned flow cells, two-color chemistry cheats,
poly-G tails when the dark cycle repeats,
PacBio circles its own read seven times,
HiFi consensus scrubs away the crimes,
Nanopore reads the wiggle of the ion through the pore,
signal to bases, modifications and more,
ultra-long strands span the repeats that hide,
Hi-C folds chromatin, optical maps the wide,
Strand-seq sorts homologs, bisulfite burns C to U,
EM-seq spares the strand — a gentler read-through.
[Bridge]
FFPE deamination fakes a C-to-T scar,
cfDNA fragments short as nucleosome bars,
low input trembles, contamination creeps in the well,
substitutions haunt Illumina, indels haunt the nanopore cell,
homopolymers trip the long-read call,
know your error profile or you'll misread it all,
replicates, controls, batch effects tracked with care,
metadata's the map — don't sequence unaware.
[Verse 4]
Lander-Waterman whispers the coverage you're owed,
thirty-fold times one-fifty base reads down the road,
divide by genome length, that's your lambda born,
e to the negative lambda — the lacuna left unworn,
a lacuna's a gap, a silence in the sea,
solve that fraction and you'll know your blind spot's decree,
three-point-one gigabases, run the numbers straight,
plan your depth before you seal the plate.
7. Module 5 — Sequence Data Formats & Tooling (Week 9)
[Verse 1]
Four letters, one code, A-T-G-C stacking tight,
FASTA's the header, the greater-than sign starts the flight,
Quality's silent there, just sequence, clean and bare,
But FASTQ adds a heartbeat — four lines, handle with care,
Plus sign, then the Phred string, ASCII plus thirty-three,
Q equals minus ten log of the error probability,
Q forty means one in ten thousand miss,
Samtools faidx indexes it, seqkit checks what you dismissed.
[Chorus]
Ich lese die Basen, Zeile für Zeile,
FASTA, FASTQ — ich brauch keine Eile,
Null-based, half-open, das Bett auf der Bank,
One-based, closed like VCF — merk dir den Gedanke!
Format für Format, ich knack den Code,
Sequenzen, Signale — das ist mein Modus,
Samtools, bedtools, mein Werkzeugkasten singt,
Genom für Genom, bis die Wahrheit klingt.
[Verse 2]
SAM flag ninety-nine — paired, mapped, mate reversed too,
Flag one-forty-seven closes the pair, that's the read-two crew,
Decode it by hand, then check with samtools flags,
Binary whispers hiding in decimal tags,
CIGAR walks the alignment — M for match, D deletes,
I is insertion, S is soft-clip where the read retreats,
Sum the M's and D's for the reference span you chase,
NM counts mismatches, MD writes the string in place.
[Verse 3]
BED starts at zero, half-open like a door left cracked,
Chromosome one position zero is really base one, fact,
But VCF and GFF close it, one-based, no gap between,
Off-by-one's the gremlin every pipeline's seen,
Convert BED to VCF? Add one to where you stand,
Test your edges — empty intervals, the start and end that band,
BGZF zips it, tabix builds the index key,
CSI for the big ones, BAI for the referee.
[Bridge]
GRCh37 flirts with chr, no chr, thirty-eight,
T2T closes gaps that thirty-seven left to fate,
LiftOver drags coordinates across the build divide,
Some variants fall in decoys — CrossMap tells you where they died,
Alt contigs, patched regions, names that don't align,
Check your reference twice, or the whole call set's a landmine.
[Verse 4]
GFA links the nodes, a graph instead of line,
Gfatools and vg walk the pangenome design,
PAF's the lightweight cousin, minimap2's quick report,
MAF stacks the species, CHAIN's the liftover's escort,
POD5 holds the current, FAST5's aging kin,
Modkit reads the MM and ML tags tucked within,
Unaligned BAM still carries modification's trace,
Every tool, every format — know its purpose, know its place.
[Chorus]
Ich lese die Basen, Zeile für Zeile,
FASTA, FASTQ — ich brauch keine Eile,
Null-based, half-open, das Bett auf der Bank,
One-based, closed like VCF — merk dir den Gedanke!
Format für Format, ich knack den Code,
Sequenzen, Signale — das ist mein Modus,
Samtools, bedtools, mein Werkzeugkasten singt,
Genom für Genom, bis die Wahrheit klingt.
[Outro]
Zero to closed, closed back to zero,
Decode the flag, be your own hero,
Every header, every tag, every byte compressed,
Modul fünf, verstanden — jetzt kommt der nächste Test.
8. Module 6 — Sequence Algorithms I: Alignment (Weeks 10–11)
[Verse 1]
Two strands drift apart, I build a grid to bring 'em close,
Every cell's a choice—match, mismatch, gap, or ghost.
Needleman-Wunsch runs corner to corner, stretched out global,
Smith-Waterman digs a pocket, keeps the local node so noble.
Semi-global splits the difference, no penalty on loose ends,
Traceback arrows crawl uphill to where the story bends.
[Chorus]
N-W goes end to end, S-W finds the hidden gem,
Gap open, gap extend, Gotoh's curve bends the stem,
BWT flips the text, FM-index skips the mess,
Seed it, chain it, score it—alphabet of yes.
[Verse 2]
Scoring matrix whispers what a swap is really worth,
BLOSUM counts survivable swaps since protein birth,
DNA keeps it simple, match plus, mismatch minus,
Affine gaps say opening costs more than staying, Gotoh finds us.
Three matrices in motion—insertion, deletion, match,
Karlin-Altschul tells you if your score's a lucky catch.
E-value counts the hits by chance across the raw,
BLAST seeds an eleven-mer, extends it, bends the law.
[Chorus]
[Verse 3]
Clustal builds a tree then aligns branch by branch, greedy and progressive,
MAFFT and MUSCLE loop back till the columns turn impressive,
T-Coffee blends libraries of pairs for consistency's sake,
Trim the ragged edges out before the model starts to shake.
Suffix array sorts every rotation, orderly and slow,
Burrows-Wheeler scrambles letters, clusters where the last chars go,
FM-index rides that transform, backward search walks right to left,
Count and locate, ranked in blocks—memory's a lighter heft.
[Verse 4]
Minimizers skim the k-mers, keep the smallest in the frame,
Sparse but sturdy seeds for chaining, minimap2's whole game.
Chain the anchors into arcs, colinear and lean,
BWA-MEM and Bowtie2 run that seed-and-extend machine.
Introns split the RNA read, spliced alignment bends the arc,
Multi-mapping muddies MAPQ, repeats leave a foggy mark.
Bismark turns the C to T, bisulfite rewrites the code,
Sort the BAM, mark duplicates, recalibrate the load.
[Verse 5]
Hidden Markov models hum through profile states unseen,
Match, insert, delete transitions weave the hidden scene.
Viterbi walks the likeliest path, forward-backward sums the rest,
Pfam builds its domains from the model that scores best.
De Bruijn graphs assemble reads where k-mers overlap and merge,
Contigs rise from tangled paths where branching edges converge.
[Bridge]
Every gap's a decision, every seed's a bet,
Score it, chain it, prove it—statistics is the net.
From matrix cell to BWT rank, the logic never bends,
Alignment's the language where a genome's story ends.
[Chorus]
N-W goes end to end, S-W finds the hidden gem,
Gap open, gap extend, Gotoh's curve bends the stem,
BWT flips the text, FM-index skips the mess,
Seed it, chain it, score it—alphabet of yes.
[Outro]
Close the traceback, close the trap,
That's the whole cerebral map.
9. Module 7 — Sequence Algorithms II: Assembly, k-mers & Sketching (Weeks 12–13)
[Verse 1]
Take a genome, shred it into overlapping little strings,
Lay them end to end and let the matching edges sing,
That's overlap, layout, consensus — O-L-C by name,
Building genomes like a jigsaw missing half its frame.
Switch the lens now, chop each read to k-mer bites instead,
String the nodes where k-minus-one letters overlap and spread,
That's a de Bruijn graph, and if the copies all ran clean,
One Eulerian path walks through and shows you what it's seen.
But errors twist the picture, bubbles bloom where bases lied,
Tips are dead-end alleys — snip them off and let them slide.
[Chorus]
O-L-C, then de Bruijn, Euler ties the thread,
Trim the tips and pop the bubbles, chase the graph ahead,
Repeats are the ceiling, read length breaks the wall,
Count your k-mers, sketch your hash — that's how we cover all.
[Verse 2]
Repeats are the palimpsest — a page erased and written twice,
same sequence laid on old sequence, no seam to tell the price,
Short reads stumble in that overlap, lost inside the maze,
SPAdes and MEGAHIT dig short contigs from the haze,
Long reads stretch clean across the trap like a bridge above a creek,
Hifiasm, Flye, and Verkko chase the telomere's far peak,
Haplotypes unbraided now, both parents' strands laid bare,
Telomere to telomere — the whole map, end to end, no tear.
[Verse 3]
Hi-C throws a net of contacts, folds the draft into shape,
Optical maps mark the mileposts, scaffolds start to take,
Polish every letter twice till the consensus base is sure,
Then measure what you've built — is the finished genome pure,
N50's the median brick, NG50 corrects for scope,
auNG draws the whole curve out — the area under hope,
BUSCO counts the genes you'd bet on always keeping near,
Merqury grades your QV, QUAST hunts trouble in the gear.
[Chorus]
O-L-C, then de Bruijn, Euler ties the thread,
Trim the tips and pop the bubbles, chase the graph ahead,
Repeats are the ceiling, read length breaks the wall,
Count your k-mers, sketch your hash — that's how we cover all.
[Verse 4]
Jellyfish and KMC, they're counting every k-mer chord,
Plot the spectrum, find the peaks, let GenomeScope afford
A guess at genome size and how heterozygous you run —
Two peaks mean two haplotypes, one lonely peak means one.
Bloom filters hold a rumor, space-cheap, might swear "it's there,"
Count-min sketch remembers tallies without the full affair,
MinHash grabs the smallest hashes, FracMinHash keeps a share,
Mash and sourmash cluster genomes — ANI tells who's kin to spare.
[Bridge]
Mask the repeats first so genes don't hide behind the weeds,
AUGUSTUS and Prodigal predict from raw ab initio seeds,
BRAKER blends the evidence, RNA proof and homology,
Function tags get stitched on last — that's the whole biology.
[Chorus]
O-L-C, then de Bruijn, Euler ties the thread,
Trim the tips and pop the bubbles, chase the graph ahead,
Repeats are the ceiling, read length breaks the wall,
Count your k-mers, sketch your hash — that's how we cover all.
10. Module 8 — Variant Discovery & Genotyping (Weeks 14–16)
[Verse 1] (Male)
Pileup stacked like witnesses, quality scores testifying,
each read's a juror, Phred's the judge decrying,
genotype likelihood — the data given the type,
multiply the errors till the posterior's ripe,
Bayes walks in with a prior on his shoulder,
Hardy-Weinberg whispers how the alleles get older,
bcftools counts columns, HaplotypeCaller rebuilds instead—
local reassembly don't trust the pile, it walks the graph ahead.
[Chorus]
Pileup or assemble, pick your witness stand,
prior meets the likelihood, posterior in hand,
joint call the cohort, gVCF's the bridge,
filter out the liars from the ridge to the ridge—
QD and strand bias, allele balance don't lie,
hard filters or VQSR, teach the model why.
[Verse 2] (Female)
DeepVariant reads the pileup like a photograph,
convolutions scanning for the variant epitaph,
Clair3 rides the long reads, context is the key,
neural nets replacing the simple MLE,
cohorts bank in gVCF, block by silent block,
GenotypeGVCFs turns that bank into a stock,
rare variants get rescued once the priors tighten up—
but low QD's a red flag, don't drink from that cup.
[Chorus]
Pileup or assemble, pick your witness stand,
prior meets the likelihood, posterior in hand,
joint call the cohort, gVCF's the bridge,
filter out the liars from the ridge to the ridge—
QD and strand bias, allele balance don't lie,
hard filters or VQSR, teach the model why.
[Verse 3] (Male)
Tumor next to normal, subtraction tells the story,
Mutect2 hunts the somatic, low VAF, no glory,
panel of normals scrubs the sequencer's scars,
FFPE fakes a mutation, oxidation draws its bars,
Strelka2 races clean, somatic and precise,
purity and ploidy — the ASCAT roll of dice,
subclones hide in fractions, point-oh-five to spare,
cancer's a population evolving unaware.
[Verse 4] (Female)
Structural variants brawl in four kinds of evidence—
split reads snap in half, discordant pairs make sense,
Manta stitches seams, Delly counts the pairs,
Sniffles rides long reads where cuteSV repairs,
CNVkit normalizes GC, segments what we see,
CBS carves the genome, Markov walks it free,
ExpansionHunter counts the triplet, repeat by repeat,
WhatsHap phases reads, trios make it complete.
[Bridge]
(Male) Left-align the indel, vt and bcftools norm it,
(Female) same mutation, different clothes — decompose, transform it,
(Both) GIAB's the mirror, hap.py grades the test,
precision, recall, F1 — stratify the rest,
homopolymers, segdups, the regions called "hard"—
truth is not one number, it's context, it's a guard.
[Chorus]
Pileup or assemble, pick your witness stand,
prior meets the likelihood, posterior in hand,
joint call the cohort, gVCF's the bridge,
filter out the liars from the ridge to the ridge—
QD and strand bias, allele balance don't lie,
hard filters or VQSR, teach the model why.
11. Module 9 — Variant Interpretation & Annotation (Week 17)
[Verse 1]
A raw VCF is just a rumor in the dark,
run it through VEP, SnpEff, ANNOVAR — three tools mark
the same lone base with different tongues that speak,
Sequence Ontology gives the syntax that we seek.
Missense, nonsense, frameshift, splice site call,
HGVS writes it clean: c dot, p dot, that's the crawl
from DNA to protein, one transcript, one truth—
MANE Select's the elder that we lean on for proof.
[Chorus]
Annotate, filter, classify — that's the chain,
gnomAD tells you common, ClinVar tells you pain,
VEP finds the letter, ACMG finds the weight,
five tiers of certainty from benign to fate:
pathogenic, likely, uncertain, likely benign, benign — remember that.
[Verse 2]
Before you cry disease you check who else is well,
gnomAD's a hundred forty thousand genomes to tell
if your "rare" mutation's hiding in plain sight—
dbSNP remembers names, 1000 Genomes gives sight
across the continents, allele frequency's the sieve,
one percent and rising means that phenotype won't live
in patients that you're chasing, so filter first, then think,
constraint before conviction, that's the researcher's link.
[Chorus]
Annotate, filter, classify — that's the chain,
gnomAD tells you common, ClinVar tells you pain,
VEP finds the letter, ACMG finds the weight,
five tiers of certainty from benign to fate:
pathogenic, likely, uncertain, likely benign, benign — remember that.
[Verse 3]
ClinVar's the courtroom where the submitted evidence piles,
OMIM's the family tree of genes and inherited trials,
ClinGen curates the panels, tells you what gene's real—
then ACMG and AMP hand you the classification wheel:
PVS1 for null variants, PM2 for rare and quiet,
PP3 computational, BS2 the healthy-carrier alibi.
Richards wrote the rulebook back in twenty fifteen ink,
document your evidence or the reviewers make you sink.
[Bridge]
CADD scores the damage deep, REVEL refines the missense guess,
AlphaMissense folds the protein, reads the fold's distress,
SpliceAI hears the intron whisper where the cut should be,
pLI and LOEUF measure how a gene stays whole when it goes empty—
the closer LOEUF creeps to zero, the less that gene can fail,
constraint is just the body counting losses down the trail.
[Verse 4]
Not every letter lives inside a coding exon's frame—
ENCODE's cCREs mark switches with no protein name,
GTEx runs the eQTLs, ties a variant to expression's drop,
regulatory reading is the harder puzzle-stop.
PharmGKB and CPIC tell you how the body clears the pill,
CYP2D6 slow or fast decides if dosage cures or kills.
And when you find the thing that nobody asked to know,
ethics asks you: who consented, and who gets to say so?
[Chorus]
Annotate, filter, classify — that's the chain,
gnomAD tells you common, ClinVar tells you pain,
VEP finds the letter, ACMG finds the weight,
five tiers of certainty from benign to fate:
pathogenic, likely, uncertain, likely benign, benign — remember that.
12. Module 10 — Population & Evolutionary Genomics (Weeks 18–20)
[Verse 1]
Count alleles like coins tossed in the wind,
Hardy and Weinberg drew the calm within—
p squared, two p q, q squared, the trio holds still,
till drift comes shaking the frequency's will.
Wright-Fisher spins a wheel of finite seed,
Moran swaps one soul at a time, and we proceed,
effective size N-e, the population's true heart,
smaller than the census count, drift plays its part.
[Chorus]
Count the alleles, p and q entwined,
Pi and Watterson's Theta, diversity defined,
Tajima's D tells if the tree runs cold or hot,
drift or selection—know which one, and which is not.
[Verse 2]
Coalescent traces lineages back through time,
two branches close and merge—that's the coalescent rhyme.
Site frequency spectrum, a histogram of age,
rare mutations young, the common ones the sage.
Pi counts the pairwise differences we find,
Theta Watterson counts segregating sites combined,
when the two disagree, Tajima's D will confess
a bottleneck's shadow or a sweep's caress.
D-prime and r-squared measure linkage's tight embrace,
distance breaks the bond, the haplotype block loses face.
[Chorus]
[Verse 3]
FST splits the globe, populations drawn apart,
PCA plots the drift map on a genomic chart,
ADMIXTURE paints ancestry in colored bars of proof,
D-statistics whisper if ghosts once shared a roof.
dN over dS, the ratio of change,
McDonald-Kreitman sorts the neutral from the strange,
iHS and XP-EHH hunt the sweep's long tail,
background selection thins the diversity sail.
[Verse 4]
PSMC reads coalescence deep in the past,
msprime and SLiM simulate what bone can't forecast,
tsinfer and Relate rebuild the ancestral graph entire,
Jukes-Cantor, Kimura, HKY, GTR plus gamma's fire.
Maximum likelihood and Bayesian trees compete,
bootstrap the branches, ask if they'd survive repeat,
gene trees dodge species trees when lineages sort askew,
incomplete lineage sorting muddies who begat who.
Synteny and orthology map the shared blueprint,
phyloP and phastCons score what conservation meant,
ancient DNA, brittle strands of frozen kin,
whispering how populations wandered, and where they've been.
[Verse 5]
Quantitative traits bow to polygenic score,
GWAS hunts the variants hiding at the core,
heritability splits the nature from the nurture's claim,
epistasis tangles credit, no locus wins alone the fame.
Recombination shuffles the deck with every generation's turn,
hotspots mark the places where the chromosomes churn,
mutation-selection balance keeps the rare disease alive,
purifying selection prunes what can't survive.
[Bridge]
Every genome's a manuscript of drift and design,
copied errors, copied loves, copied down the line,
we read the letters, count the ghosts inside the tree,
the coalescent hums the oldest melody.
[Chorus]
[Outro]
p squared, two pq, q squared—say it till it's true,
Pi and Watterson's Theta, Tajima's D too,
FST, PCA, the sweep and the clock,
population genomics—read it in the rock.
13. Module 11 — Statistical Genetics & Association (Weeks 21–22)
[Verse 1]
Grandma's eyes skip a generation — recessive hides down low,
Pedigree's the family map, autosomal or X, we trace the flow,
Penetrance ain't a promise, carry the gene and still dodge the show,
LOD score hits a three, that's a thousand-to-one — linkage locked, now we know.
[Chorus]
C'est dans les gènes, chérie, l'héritage qui parle,
Statistique, mon amour, on cherche la trace, on cherche la marque,
P less than five times ten to the negative eight — that's the genome-wide gate,
Décode le code, mon cœur, décode le destin, ne débat pas.
[Verse 2]
Cases and controls, a million markers on parade,
Call rate ninety-nine, Hardy-Weinberg keeps the drift delayed,
Check the sex chromosomes, check who's kin, PCA clears the haze,
REGENIE, SAIGE, BOLT-LMM — mixed models tame the maze.
Stratification's a liar wearing ancestry's disguise,
Ten components deep, we strip the bluff before it wins the prize.
[Verse 3]
Bonferroni's stingy, divide alpha 'til it's thin,
Five times ten negative eight — the genome-wide gate lets few peaks in,
FDR's the gentler judge, Benjamini keeps the false discovery slim,
TOPMed's the deep well, Minimac and IMPUTE5 fill in every limb.
Twins split at birth still echo the same disease refrain,
GCTA-GREML, LDSC pull heritability straight out the summary chain.
[Chorus]
C'est dans les gènes, chérie, l'héritage qui parle,
Statistique, mon amour, on cherche la trace, on cherche la marque,
P less than five times ten to the negative eight — that's the genome-wide gate,
Décode le code, mon cœur, décode le destin, ne débat pas.
[Verse 4]
SuSiE narrows the block down to a credible set, tight and small,
FINEMAP bets on the causal one when ten variants stand tall,
Coloc checks if the GWAS peak and the eQTL share one flame,
TWAS wires expression straight to trait — same signal, different name.
One rare variant alone just whispers, statistically it's weak,
So SKAT and SKAT-O bundle the whispers 'til the burden starts to speak.
[Bridge]
Polygenic score — sum the weighted risk, but ancestry can betray it,
Cross the continent, portability drops, recalibrate to save it,
Mendelian randomization: instrument, exposure, outcome in a line,
Pleiotropy sneaks in sideways — check your assumptions before you sign.
[Chorus]
C'est dans les gènes, chérie, l'héritage qui parle,
Statistique, mon amour, on cherche la trace, on cherche la marque,
P less than five times ten to the negative eight — that's the genome-wide gate,
Décode le code, mon cœur, décode le destin, ne débat pas.
[Outro]
Manhattan skyline made of peaks, QQ plot keeps us honest, lambda close to one —
Ma chérie, la trace est là, l'histoire du génome est écrite, mais jamais finie.
14. Module 12 — Epigenomics & Functional DNA Assays (Weeks 23–24)
[Verse 1]
Cytosine wearing a shadow, methyl tag on its back,
CpG islands cluster where the shores start to crack,
Bisulfite melts the code, unmethylated bases turn,
Bismark reads the ashes, MethylDackel counts what burns,
EPIC array checks the same spot a million times over,
Long reads with modkit call it straight, no chemical cover,
DSS and methylKit trace the drift zone, the DMR,
Epigenetic clock ticking — tells your cells how old they are.
[Chorus]
CpG, TSS, follow the trail,
Methyl mark the silence, open chromatin exhale,
Peaks and loops and motifs, structure hides in the strand,
Read the shadow on the genome, computational hand.
[Verse 2]
Tn5 cuts where the nucleosome ain't holding tight,
ATAC-seq maps the open rooms, DNase does the same fight,
Fragment size periodicity — a hundred-and-forty-seven hum,
Mitochondrial reads get filtered, only nuclear signal come,
FRiP tells you the fraction landed where it should,
TSS enrichment spikes up if your prep's actually good.
[Verse 3]
ChIP-seq drags the antibody, CUT&RUN cuts closer in,
CUT&Tag tags it directly, thinner background, thinner skin,
MACS3 calls the summits, IDR checks if they're true twice,
Blacklist regions flagged — mapping artifacts, not nice,
PWM built from aligned sites, information content tall,
Logo towers where it's certain, flat where letters could fall,
MEME and HOMER discover, FIMO scans the line,
JASPAR keeps the library — motif matched, promoter fine.
[Verse 4]
Hi-C crumples the chromosome, Micro-C zooms in tighter,
Contact matrix counts collisions, ICE makes the bias lighter,
Eigenvector splits the genome, A compartment, B compartment too,
TADs are neighborhoods, loops are handshakes holding through,
Cooler stores it, cooltools reads it, Juicer squeezes the file down,
Structure folded in the nucleus, invisible in town.
[Bridge]
Single cell ATAC, one nucleus, one accessible map,
Single cell DNA-seq counts the copy number gap,
Basenji, Enformer, transformers reading far,
Attribution maps the pixel, TF-MoDISco finds the scar,
In-silico mutagenesis — flip a base, watch it react,
The model dreams in adenine and calls it fact.
[Verse 5]
VCF holds the variants, GATK calls them clean,
Phasing haplotypes together, linkage disequilibrium seen,
GWAS scans a million snips, Manhattan plots peak high,
Fine-mapping narrows credible sets, causal signal don't lie,
eQTLs link the variant to the gene it moves,
Colocalization checks the peaks, causal path it proves.
[Chorus]
CpG, TSS, follow the trail,
Methyl mark the silence, open chromatin exhale,
Peaks and loops and motifs, structure hides in the strand,
Read the shadow on the genome, computational hand.
[Outro]
Methyl, motif, matrix, fold —
the strand keeps a story that computation told.
15. Module 13 — Metagenomics, Pangenomics & Special Topics (Weeks 25–26)
[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.
16. Module 14 — Reproducibility, Scale & Capstone (Weeks 27–30)
[Verse 1]
Snakemake rules chained like dominoes falling in line,
Nextflow channels pumping data down the pipe just fine,
nf-core hands you pipelines built by a hundred hands,
WDL scripts run on Cromwell, portable where it lands,
Containers pack the runtime so it never drifts or breaks,
Docker or Singularity — pick the box the project takes,
No more "worked on my laptop" — that excuse is dead,
Reproducible means a stranger gets your same output instead.
[Chorus]
F-A-I-R, that's the flag we fly,
Findable, Accessible, Interoperable, don't ask why,
Reusable data, tested code, a pipeline built to run,
Snakemake, Nextflow, Cromwell — three roads, same sun,
Test it small before you scale it tall,
Capstone calling, gonna answer the call.
[Verse 2]
Write a unit test before you trust a single line,
Toy FASTQ with ten reads, checks the answer every time,
Continuous integration, GitHub Actions on the clock,
Every push gets vetted, every merge request gets rocked,
Small test data, minutes not hours, running end to end,
Green checkmark or you're debugging till the weekend,
Assertions catch the silent bug before it hits the wild,
Trust but verify — that's the rule for every child.
[Verse 3]
Streaming beats loading when the genome's ninety gig,
Don't read the whole BAM file, that's an amateur's gig,
htslib bindings, pysam whispers to the C,
Vectorize with NumPy, let the loops run free,
Profile your memory, find the leak before it drowns you,
Parallelize across the cores, let the cluster crown you,
Rust and C step in when Python starts to crawl,
Compiled speed for inner loops, that's the protocol.
[Verse 4]
SRA, ENA, GEO — the data's public, free,
dbGaP and EGA guard the human pedigree,
Controlled access, consent forms, re-identification fear,
A genotype can name a face if you're not careful here,
MINSEQE keeps the metadata telling the story straight,
Privacy before publication — that's a scientist's trait.
[Bridge]
IGV pulls up the pileup, JBrowse renders the track,
UCSC browser shows the variant calling back,
Figures clean, reports honest — methods, limits, QC too,
Pick your capstone: germline VCF or a genome brand new,
Bacteria assembled, AMR genes in the frame,
Selection scans on populations, ATAC calling the flame,
Tumor-normal variants, signatures inked in the scar,
Six deliverables, one repo — that's how you go far.
[Chorus]
F-A-I-R, that's the flag we fly,
Findable, Accessible, Interoperable, don't ask why,
Reusable data, tested code, a pipeline built to run,
Snakemake, Nextflow, Cromwell — three roads, same sun,
Test it small before you scale it tall,
Capstone calling, gonna answer the call.
[Outro]
README open, environment locked, the license clear,
Push the final commit, thirty weeks landed here,
From double helix theory to a report that ships,
That's the DNA curriculum, mic drop, fingertips.
17. Appendix A — Mathematical & Statistical Foundations (reference track)
[Verse 1]
Flip the genome like a coin, binomial counts the reads,
Poisson catches rare mutations scattered in the weeds,
Negative binomial when the variance runs too wide,
Beta's the conjugate that keeps the prior on your side,
Likelihood's the story that the data wants to tell,
Maximize it, climb the hill, till the slope levels well,
Bayes flips the conditional, prior meets the odds,
Posterior's the answer, not from magic — just from logs.
[Chorus]
Prior times likelihood, divided by the evidence you find,
That's posterior — Bayes rewiring what you thought you'd mined,
One-step memory, the Markov chain forgets the rest,
Forward adds the maybes, Viterbi picks the best.
[Verse 2]
Markov chain's got amnesia, only last state matters most,
Hidden Markov hides the truth behind an emission ghost,
Forward algorithm sums the paths that could've made the sound,
Viterbi carves the single trail, the max path homeward bound,
Baum-Welch trains it blindfold, no labels, just the churn,
Guess it, weigh it, sharpen it — repeat until it learns,
Exon, intron, splice site — gene finders walk the seam,
CNV segments gain from loss, profile HMMs thread the theme.
[Chorus]
Prior times likelihood, divided by the evidence you find,
That's posterior — Bayes rewiring what you thought you'd mined,
One-step memory, the Markov chain forgets the rest,
Forward adds the maybes, Viterbi picks the best.
[Verse 3]
Entropy counts the bits of surprise inside a site,
Low where columns are conserved, high where anything's alright,
KL divergence clocks how far two distributions drift,
Mutual information links a motif to its cognate shift,
Null versus story you hoped true — that's the hypothesis game,
Bonferroni cuts the herd, guards against the false-claim shame,
Benjamini-Hochberg ranks and lets discovery breathe,
GLMs bend the fit to Poisson, binomial, past belief,
Mixed models add the random slope for batch and lab and day,
Permute the labels, bootstrap the sample, let the noise give way,
EM alternates forever — expect it, then maximize,
Hidden variables surface like a truth behind disguise.
[Verse 4]
PCA rotates the cloud to find the widest thread,
SVD splits the matrix into rotate, scale, and spread,
NMF stays strictly positive — signatures untangle clean,
Random forests vote in crowds, each tree a different scene,
CNNs slide a kernel, learning motifs pixel-wise,
Transformers weigh attention, every base sees every prize,
Lasso zeroes out the weights, ridge just shrinks them thin,
Split by chromosome, not sequence — or your leakage sneaks back in.
18. Appendix B — Molecular Biology Fast Track (for CS/math backgrounds)
[Verse 1]
Prokaryote's simple, no nucleus in sight,
DNA floats loose in the cytoplasm night,
E. coli style, one room, no inside walls,
Eukaryote's fancier, membrane hallways and halls,
Nucleus locked up like a vault with a code,
Mitochondria's the powerhouse, ATP's the load,
ER folds proteins, Golgi ships the freight,
Ribosomes read codons — that's translation's estate.
[Chorus]
Célula, célula, minha pequena fábrica,
DNA to RNA to proteína, es la lógica,
Núcleo é a oficina, citoplasma é el mar,
Compartimento certo pra cada function, ¿está claro?
[Verse 2]
RNA polymerase reads the template line,
Builds a message strand, mRNA design,
Cap goes on front like a crown, five-prime,
Poly-A tail stitched on, keeping perfect time,
Introns get spliced out, exons glued as one,
Spliceosome's the tailor, cutting till it's done,
Ribosome grabs the code, reads it three by three,
tRNA drops amino acids, building endlessly.
[Verse 3]
Promoter's the doorbell right before the gene,
Transcription factors knock, say what they mean,
Enhancers work far off, then loop back like a string,
Chromatin's the wrapping, histones do their thing,
Wind it tight, it's silent, loosen up, it sings,
Acetyl marks say "open," methyl closes wings,
Epigenetic switches, same code, different tune,
Regulation's the reason skin cells don't grow plumes.
[Chorus]
Célula, célula, minha pequena fábrica,
DNA to RNA to proteína, es la lógica,
Núcleo é a oficina, citoplasma é el mar,
Compartimento certo pra cada function, ¿está claro?
[Bridge]
E. coli in a flask, teaches genetics fast,
Yeast buds off copies, cell cycle unsurpassed,
C. elegans transparent, watch the neurons grow,
Drosophila's wings chart every gene in a row,
Zebrafish see-through, development on parade,
Mouse shares our genome, ninety-nine percent, no shade,
Arabidopsis, quiet weed, plant biology's friend,
Cada organismo, uma lição sem fin.
[Verse 4]
Twenty amino acids, beads upon a string,
Fold into domains, doing their functioning thing,
Alpha helix twists, beta sheet lays flat,
Tertiary structure is the final acrobat,
Mendel's peas showed dominant and recessive genes,
Alleles segregate — meiosis splits the scenes,
Halves the chromosome count, precise and clean,
Crossing over shuffles cards, recombination's routine,
Linked genes stick close, rarely split apart,
Map units count the distance — genetics is an art.
[Chorus]
Célula, célula, minha pequena fábrica,
DNA to RNA to proteína, es la lógica,
Núcleo é a oficina, citoplasma é el mar,
Compartimento certo pra cada function, ¿está claro?
[Outro]
Da célula ao gene, do gene à proteína,
Agora fala a língua — biología divina,
Fast track finished, class dismissed, chau chau,
DNA to RNA to proteína, vamos now.
19. Appendix C — Core Tool Checklist
[Verse 1]
Male: seqkit slice, seqtk trims the fat,
Biopython scripting, pyfaidx indexes that.
FastQC scans, MultiQC compiles the tale,
fastp cuts the crud, NanoPlot reads the long-read scale.
Female: Trimmomatic, Cutadapt, snip the adapter thread,
Clean it before you map or the whole run's dead.
[Chorus]
Male: On répète, on nettoie, on aligne — c'est la loi
Female: Проверяй качество, не спеши, друг мой
Both: Sequence, trim, align, and call,
Каждый шаг важен — that's the protocol.
C'est le workflow, du début à la fin,
Check the checklist, let the data win.
[Verse 2]
Female: BWA-MEM2 races, Bowtie2 keeps the seed,
minimap2 handles long reads at speed.
BLAST plus for homology, MAFFT lines them tight,
Male: samtools sorts, pysam reads it right,
Picard marks duplicates, mosdepth checks the reach,
bedtools intersects what the intervals teach.
pybedtools, pyranges — Python's got the range,
Female: genomic real estate, rearranged, exchanged.
[Chorus]
Male: On répète, on nettoie, on aligne — c'est la loi
Female: Проверяй качество, не спеши, друг мой
Both: Sequence, trim, align, and call,
Каждый шаг важен — that's the protocol.
[Verse 3]
Male: GATK calls germline, bcftools filters clean,
DeepVariant's neural net, Clair3 the long-read scene,
FreeBayes for populations, Mutect2 hunts the tumor's ghost,
Female: Manta finds the breakpoints, Delly's structural host,
Sniffles2 for long-read SVs, CNVkit counts the dose,
VEP, SnpEff, ANNOVAR — annotate the most.
[Bridge]
Both: SPAdes assembles, hifiasm's precise,
Flye circles genomes, QUAST rolls the dice,
BUSCO checks completeness, Merqury checks the k-mer trace,
Female: PLINK2 crunches cohorts at a breakneck pace,
msprime simulates ancestry, tskit stores the tree,
Male: REGENIE regresses traits across GWAS scenery,
IQ-TREE, RAxML-NG, BEAST dates the clade —
that's your phylogenetic panoply displayed.
[Verse 4]
Female: Bismark bisulfite, MACS3 finds the peak,
deepTools plots coverage, HOMER finds the motif's clique,
MEME Suite finds patterns, cooler holds the Hi-C map,
Male: Kraken2 classifies, MetaPhlAn fills the gap,
MetaBAT2 bins the contigs, CheckM2 checks their fate,
IGV's my lodestar — a guiding star, I navigate.
UCSC, JBrowse 2, matplotlib draws it clean,
Female: Snakemake, Nextflow — pipelines run the machine.
[Chorus]
Male: On répète, on nettoie, on aligne — c'est la loi
Female: Проверяй качество, не спеши, друг мой
Both: Sequence, trim, align, and call,
Каждый шаг важен — that's the protocol.
[Outro]
Male: Chaque outil à sa place, каждый на своём посту
Female: Check the version, read the docs — tools evolve, c'est vrai
Both: Appendix C, the checklist stays,
Core tools mastered, in a thousand ways.
20. Appendix D — Core Reading List
[Verse 1]
Durbin Eddy Krogh Mitchison, stacked on my shelf,
Biological Sequence Analysis, HMMs teach themself,
Compeau and Pevzner, algorithms drawn like a map,
Jones and Pevzner's cousin text, same lineage, different lap,
Buffalo's Data Skills, command line callus on my hand,
Holmes and Huber's stats, modern biology's grammar planned,
Hartl and Clark counting alleles drifting through the pool,
Felsenstein building trees, Alberts the cellular school.
[Chorus]
D-E-K-M, Compeau, Pevzner, Buffalo too,
Holmes Huber Hartl Clark, Felsenstein and the molecular crew,
Read the spine before you read the genome, that's the mnemonic key,
Watson Crick to T2T, stack the papers, climb the tree.
[Verse 2]
Fifty-three, Watson and Crick, the double helix unspooled,
Sanger seventy-seven, chain terminator ruled,
Ninety, Altschul's BLAST came burning through the database night,
Two-thousand-one, the Consortium drafted human in sight,
Oh-nine, Li and Durbin, BWA aligning reads like thread,
Twenty-fifteen, thousand genomes, variation widespread,
Twenty-two, Nurk's T2T, telomere to telomere sewn whole,
Twenty-three, Liao's pangenome — not one map but a chorus of scrolls.
[Chorus]
D-E-K-M, Compeau, Pevzner, Buffalo too,
Holmes Huber Hartl Clark, Felsenstein and the molecular crew,
Read the spine before you read the genome, that's the mnemonic key,
Watson Crick to T2T, stack the papers, climb the tree.
[Verse 3]
Langmead's lectures, algorithms for the DNA sequencing grind,
Rosalind dot info, problems one-two, six-seven aligned,
Sanger EMBL-EBI training, Galaxy's friendly frame,
Nf-core and Snakemake, pipelines that remember your name.
Every genome's a palimpsest, old writing under new,
Layers of ancestor code the sequencers still push through,
Read the elders before you build, that's the sedulous way,
Diligent, careful, patient — building block by block each day.
[Bridge]
Eight books, eight papers, four courses, one long thread,
Every citation a rung where the ladder's led,
I didn't invent this, I'm just passing down the key,
Durbin to Nurk to you — that's the whole family tree.
[Chorus]
D-E-K-M, Compeau, Pevzner, Buffalo too,
Holmes Huber Hartl Clark, Felsenstein and the molecular crew,
Read the spine before you read the genome, that's the mnemonic key,
Watson Crick to T2T, stack the papers, climb the tree.
[Outro]
D-E-K-M, Compeau, Pevzner, Buffalo too,
Watson to Liao, the reading list carries you,
Close the book, open the terminal, let the genome sing,
Appendix D remembered — that's the whole offering.
21. Self-Assessment: You're "Fluent" When You Can…
[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.
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