> For the complete documentation index, see [llms.txt](https://jodyphelan.gitbook.io/tutorials/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://jodyphelan.gitbook.io/tutorials/ngs.md).

# NGS

- [Sample QC](https://jodyphelan.gitbook.io/tutorials/ngs/sample-qc.md)
- [Consensus building](https://jodyphelan.gitbook.io/tutorials/ngs/consensus-building.md): This page describes a basic procedure to generate consensus sequences
- [FastQ to VCF](https://jodyphelan.gitbook.io/tutorials/ngs/fastq-to-vcf.md): This page describes the pipeline to go all the way from fastq data to a merged multi-sample VCF
- [Mapping pipeline](https://jodyphelan.gitbook.io/tutorials/ngs/mapping-pipeline.md)
- [Fst with delly](https://jodyphelan.gitbook.io/tutorials/ngs/fst-with-delly.md)
- [Kraken2](https://jodyphelan.gitbook.io/tutorials/ngs/kraken2.md)