# 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 %}


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://docs.kbase.us/workflows/assembly-annotation.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.