Expert-level genomics covering whole genome sequencing, genome assembly, annotation, comparative genomics, functional genomics, single-cell genomics, and multi-omics integration.
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Short-read: Illumina — high accuracy, low cost, 150-300bp reads. Long-read: PacBio (SMRT), Oxford Nanopore — spans repeats, structural variants. Hi-C: chromatin conformation, scaffolding assemblies. Single-cell: 10x Genomics, Drop-seq — individual cell transcriptomes.
De novo assembly: overlap-layout-consensus, de Bruijn graphs. Tools: SPAdes (short-read), Flye (long-read), Hifiasm (HiFi). Assembly metrics: N50, L50, contig count, genome completeness (BUSCO). Scaffolding: Hi-C, optical mapping, genetic maps.
Structural annotation: gene prediction (Augustus, MAKER), repeat masking (RepeatMasker). Functional annotation: BLAST, InterPro, GO terms, KEGG pathways. Non-coding elements: promoters, enhancers, regulatory regions. Comparative annotation: synteny, ortholog identification.
SNVs and indels: GATK HaplotypeCaller, DeepVariant. Structural variants: Manta, LUMPY, PBSV. Copy number variants: CNVkit, Control-FREEC. Variant filtering: VQSR, hard filters, population frequency.
RNA-seq: transcript quantification, differential expression (DESeq2, edgeR). ChIP-seq: protein-DNA binding, peak calling (MACS2). ATAC-seq: chromatin accessibility, open chromatin regions. Metagenomics: community profiling, functional annotation of environmental samples.
| Pitfall | Fix |
|---|---|
| Low coverage causing false variants | Aim for 30x minimum for WGS |
| Repeat regions causing assembly gaps | Use long reads to span repeats |
| Contamination in assemblies | Run BLAST against contaminant databases |
| Ignoring batch effects in RNA-seq | Include batch as covariate in model |
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Expert-level abstract algebra knowledge. Use when working with groups, rings, fields, modules, Galois theory, representation theory, or algebraic structures. Also use when the user mentions 'group', 'ring', 'field', 'homomorphism', 'isomorphism', 'normal subgroup', 'quotient group', 'Sylow theorem', 'Galois theory', 'polynomial ring', 'ideal', 'module', 'vector space', or 'representation theory'.
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Expert-level acoustics knowledge. Use when working with sound waves, acoustic propagation, resonance, standing waves, Doppler effect, room acoustics, ultrasound, noise control, musical acoustics, or architectural acoustics. Also use when the user mentions 'sound wave', 'decibel', 'frequency', 'resonance', 'standing wave', 'Doppler effect', 'acoustic impedance', 'reverberation', 'ultrasound', 'noise control', 'harmonics', or 'sound intensity'.
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Expert-level aerodynamics covering subsonic and supersonic flow, lift and drag, airfoil theory, boundary layers, compressible flow, and CFD methods.
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Expert-level air quality engineering covering pollutant sources, atmospheric dispersion, air quality standards, emission controls, and air quality modeling.
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Expert-level aircraft structures covering structural design philosophy, wing and fuselage analysis, fatigue and damage tolerance, composite structures, and certification.
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Expert-level algorithms and complexity theory covering sorting, searching, graph algorithms, dynamic programming, greedy algorithms, NP-completeness, and algorithm design paradigms.
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