[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.
← Appendix B — Molecular Biology Fast Track (for CS/math backgrounds) | Appendix D — Core Reading List →