> For the complete documentation index, see [llms.txt](https://docs.kbase.us/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.kbase.us/workflows/assembly-annotation.md).

# Assembling & Annotating Microbial Genomes

KBase enables *de novo* assembly of prokaryotic NGS reads from various sequencing platforms. Assemblies can then be annotated with RAST or Prokka, enabling you to explore structural and functional features of a Genome or use it in other analyses. 

{% hint style="info" %}
Steps for [assembly and annotation](/apps/analysis/assembly-and-annotation.md) include:

1. Upload reads to assemble.
2. [Add your Reads data object](/data/upload-download-guide/reads.md) to the Narrative.
3. Search the App Catalog and insert an [Assembly App](https://kbase.us/applist/#Genome%20Assembly) 
   * Use one of these tools to create an Assembly object.
4. Search the App Catalog and insert an [Annotation App](https://kbase.us/applist/#Genome%20Annotation)
   * Use one of these tools to annotate the Assembly object.
5. Examine assembly job statistics and genome annotation.
   {% endhint %}

## Narrative Tutorials

* [Microbial Genomics in KBase: Drafting Isolate Genomes (Short-reads)](https://narrative.kbase.us/narrative/83666) – demonstrates how to draft isolate genomes using Illumina short-read sequencing from quality assessment to assembly and annotation. 
* [Microbial Genomics: Drafting Isolate Genomes (Long-reads)](https://narrative.kbase.us/narrative/200668) – demonstrates how to draft isolate genomes using Oxford Nanoport MinION long-read sequences from quality assessment to assembly and annotation. 

## Video Tutorials

{% embed url="<https://youtu.be/EGW3rA8tWf4>" %}
Introduction to Genome Analysis
{% endembed %}

{% embed url="<https://youtu.be/W6QBVmb9vC0?si=pA8HuO51SZfECG0d>" %}
Microbial Genomics in KBase (short- and long-read examples)
{% endembed %}


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