Add skeleton documentation for Assembly Page

Author: lukekoch

docs/assets/screenshots/AssemblyPage.png

@@ -6,4 +6,4 @@ authors:
 date: 2025-06-03
 ---
 
-G-nom core is the core webb application written in [Laravel](https://laravel.com/). G-nom core handles all data storage and import and provides the base web interface. G-nom core is available in our [Github respository](https://github.com/G-nom-Project/g-nom).
+G-nom core is the core web application written in [Laravel](https://laravel.com/). G-nom core handles all data storage and import and provides the base web interface. G-nom core is available in our [Github respository](https://github.com/G-nom-Project/g-nom).

docs/assets/screenshots/AssemblyPageBUSCO.png

@@ -0,0 +1,7 @@
+Most of G-nom's functionality is tied to personal user accounts. You can create a new user account using your name and e-mail address at the URL `/register`.
+
+!!! note "Self-signup"
+
+    Admins can disable self-signup at their discretion. In this case contact your administrator to create an account manually for you.
+
+Depending on your G-nom configuration, you may receive an e-mail to verify your e-mail address.

docs/assets/screenshots/AssemblyPageBrowser.png

@@ -0,0 +1,7 @@
+![Assembly Card](../assets/screenshots/assemblycard.png){ align=left }
+
+The assembly card displays an image relevant to the taxon as well as a short, taxon-specific info text. The padlock icon next to the name indicates the public acessibility of the assembly. An open lock indicates access to all user, while a closed lock indicates access limited to the currently logged in user or their team.
+
+The corresponding assembly can be [accessed](./assembly-page.md) and bookmarked directly using the provided buttons.
+
+Availability of certain [G-nom core analyses](../plugins.md) is indicated directly on the assembly card. The BUSCO completeness score is included directly on the assembly card, while Repeatmasker and taXaminer, alongside Annotations and Mappings, are only available as counts.

docs/assets/screenshots/AssemblyPageCollapsible.png

@@ -0,0 +1,32 @@
+## Intro section
+The first section of the assembly page is made up of a grey band detailing scientific name and the custom name of the assembly. A silouette of the species can be supplied via SVG at source e.g. from [Phylopic](https://www.phylopic.org/).
+![Assembly Head](../assets/screenshots/AssemblyPage.png){ align=center }
+The first section below the band details taxon specific information. These include an image, scientifc and common names as well a short header text and longer info text. The complete NCBI lineage is displayed in a separate field.
+
+The remainder of the page is made up of four collapsible sections, which will be discussed in detail below:
+
+1. Assembly Information
+2. Annotation completeness
+3. Taxonomic classification
+4. Genome Browser
+
+## Assembly Information
+![Assembly Collapsible](../assets/screenshots/AssemblyPageCollapsible1.png){ align=center }
+The assembly information sections contains G-nom internal information as well common quality metrics and statistics. This includes sequence and contig size statistics as well as N50 and GC content. To assess the completeness of the assembly / related annotation, please check out the BUSCO and fCAT results in the next section.
+
+## Annotation completeness
+![Assembly BUSCO](../assets/screenshots/AssemblyPageBUSCO.png){ align=center }
+The annotation completeness section presents visualizations for BUSCO and fCAT results. The plot differentiates between Complete (Single-copy), Complete (Duplicated), fragmented and missing. Please refer to the documentation of the underlying tools ([BUSCO](https://busco.ezlab.org/busco_userguide.html#interpreting-the-results) | [fCat](https://f1000research.com/posters/11-1091)) for guidance on how to interpret the results.
+
+## Taxonomic assignment :material-account-hard-hat-outline:
+!!! warning taXaminer-dashboard
+
+    The taXaminer-dashboard project is currently being re-structured to be published as a singular react component. This feature should be considered unstable until the migration is complete.    
+    
+
+The taxonomic assignment section includes the complete [dashboard](https://github.com/BIONF/taxaminer-dashboard) for the visualization of taXaminer results. Additionally, it integrates with you G-nom account and the genome browser.
+
+
+## Genome Browser
+![Assembly Browser](../assets/screenshots/AssemblyPageBrowser.png){ align=center }
+The genome browser section embeds a smaller version of the [JBrowse](https://jbrowse.org/jb2/) genome browser. Per default, all available tracks will be loaded. It links to selected genes in the taXaminer dashboard, allowing you to explore the genomic neighbourhood. For detailed investigation of browser tracks, consider using the [Full-screen browser](/user-guide/browser/).