diff --git a/CHANGELOG.md b/CHANGELOG.md
index b33a1d1..1212eb4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [[PR #96](https://github.com/nf-core/pixelator/pull/96)] - Make all ext.args assignments closures
 - [[PR #98](https://github.com/nf-core/pixelator/pull/98)] - Update metromap to include layout step
+- [[PR #99](https://github.com/nf-core/pixelator/pull/99)] - Update README to include layout step
 
 ### Software dependencies
 
diff --git a/README.md b/README.md
index 1c8d8fe..fb11b3d 100644
--- a/README.md
+++ b/README.md
@@ -30,7 +30,8 @@ It takes a samplesheet as input and will process your data using `pixelator` to
 5. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator graph`](https://github.com/PixelgenTechnologies/pixelator))
 6. Call and annotate cells ([`pixelator annotate`](https://github.com/PixelgenTechnologies/pixelator))
 7. Analyze the cells for polarization and colocalization ([`pixelator analysis`](https://github.com/PixelgenTechnologies/pixelator))
-8. Report generation ([`pixelator report`](https://github.com/PixelgenTechnologies/pixelator))
+8. Generate 3D graph layouts for visualization of cells ([`pixelator layout`](https://github.com/PixelgenTechnologies/pixelator))
+9. Report generation ([`pixelator report`](https://github.com/PixelgenTechnologies/pixelator))
 
 > [!WARNING]
 > Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.
diff --git a/docs/output.md b/docs/output.md
index cda70ef..78f6f12 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -19,6 +19,7 @@ The pipeline consists of the following steps:
 - [Compute connected components](#compute-connected-components)
 - [Filtering, annotation, cell-calling](#cell-calling-filtering-and-annotation)
 - [Downstream analysis](#downstream-analysis)
+- [Generate layouts for visualization](#compute-layouts-for-visualization)
 - [Generate reports](#generate-reports)
 
 ### Preprocessing