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genome-assembly

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Genome assembly fundamentals — long-read assembly, polishing, QC metrics, and annotation.

skills/genome-assembly/SKILL.md

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## Overview

genome-assembly covers de novo genome assembly: data requirements, long-read assemblers
(HiFi and ONT), assembly QC (N50, BUSCO, k-mer completeness), scaffolding (Hi-C), polishing,
and annotation. Assembly quality determines every downstream analysis — a fragmented,
contaminated assembly poisons variant calling, annotation, and comparative genomics.

## When to use

- Planning sequencing: coverage, read type (HiFi vs ONT vs short-read), Hi-C needs.
- Assembling: hifiasm, Flye, Verkko — choosing by data type.
- QC: N50/L50, BUSCO, Merqury k-mer spectra, contamination screening.
- Scaffolding: Hi-C (YaHS, SALSA), optical maps.
- Polishing: when needed, with what reads.
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