> For the complete documentation index, see [llms.txt](https://docs.terraref.org/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.terraref.org/revisions/scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics.md).

# Experimental Design Genomics

Genomic data includes whole-genome resequencing data from the HudsonAlpha Institute for Biotechnology, Alabama for 384 samples for accessions from the sorghum Bioenergy Association Panel (BAP) and genotyping-by-sequencing (GBS) data from Kansas State University for 768 samples from a population of sorghum recombinant inbred lines (RIL).

## Whole-genome resequencing

**Experimental Design:**

* [384 BAP samples](https://github.com/terraref/documentation/tree/56f669dc870b3c3921bfc029914545574e70f8df/user/user/sorghum-lines-genomics.md) were sequenced to an average depth of \~25x.
* Shotgun sequencing (127-bp paired-end) was done using an Illumina X10 instrument at the HudsonAlpha Institute for Biotechnology.
* Variant calling was done using a [computational pipeline](https://github.com/terraref/documentation/tree/56f669dc870b3c3921bfc029914545574e70f8df/user/genomic-data-product.md) at the Danforth Center.
* See the [Data Products](https://github.com/terraref/documentation/tree/56f669dc870b3c3921bfc029914545574e70f8df/user/products/genomics-data.md) page to get access to raw and derived data products.

## Genotyping-by-sequencing

**Experimental Design:**

* [768 RIL samples](https://github.com/terraref/documentation/tree/56f669dc870b3c3921bfc029914545574e70f8df/user/user/genotyping-by-sequencing.md) were sequenced using a GBS approach.