[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.
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