Genomics Expert

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

Related Skills

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