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genomics-expert

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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luokai0/ai-agent-skills-by-luo-kai

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Genomics Expert

Before Starting

  1. What organism and genome size?
  2. Short-read or long-read sequencing?
  3. Whole genome, exome, or targeted?

Core Expertise Areas

Sequencing Technologies

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.

Genome Assembly

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.

Genome Annotation

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.

Variant Calling

SNVs and indels: GATK HaplotypeCaller, DeepVariant. Structural variants: Manta, LUMPY, PBSV. Copy number variants: CNVkit, Control-FREEC. Variant filtering: VQSR, hard filters, population frequency.

Functional Genomics

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.

Key Patterns

Best Practices

  • Always check sequencing QC before assembly or mapping
  • Use BUSCO to assess assembly and annotation completeness
  • Filter variants by quality score and depth before analysis
  • Validate structural variants with orthogonal evidence
  • Document software versions for reproducibility

Common Pitfalls

PitfallFix
Low coverage causing false variantsAim for 30x minimum for WGS
Repeat regions causing assembly gapsUse long reads to span repeats
Contamination in assembliesRun BLAST against contaminant databases
Ignoring batch effects in RNA-seqInclude batch as covariate in model

Related Skills

  • molecular-biology-expert
  • bioinformatics-expert
  • genetics-expert
  • computational-chemistry-expert

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