> For the complete documentation index, see [llms.txt](https://cgps.gitbook.io/pathogenwatch/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/genome-assembly.md).

# Genome Assembly

- [Short Read Assembly](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/genome-assembly/short-read-assembly.md): How Pathogenwatch assembles short read Illumina data