Assembling & Annotating Microbial Genomes

Running assembly and annotation in KBase

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.

Steps for assembly and annotation include:

1. Upload reads to assemble.

2. Add your Reads data object to the Narrative.

3. Search the App Catalog and insert an Assembly App

   • Use one of these tools to create an Assembly object.

4. Search the App Catalog and insert an Annotation App

   • Use one of these tools to annotate the Assembly object.

5. Examine assembly job statistics and genome annotation.

Narrative Tutorials

• Microbial Genome Assembly and Annotation Tutorial – guides through assembling a set of NGS short reads into contigs and annotate the assembled contigs, assigning biological functions derived from RAST

• Genome Analysis Tools and Features – a how-to guide for various tools to analyze genomic sequencing data in KBase from quality control and assessment of NGS reads, de novo assembly, and genome annotation

• Genome Analysis 1: Drafting Isolate Genomes – demonstrates how to draft isolate genomes from quality assessment to assembly and annotation

• Genome Analysis 2: Identifying Features of Interest in Genomes – shows how to build a workflow for searching and identifying features within your genomes

• Genome Analysis 3: Domain Annotation and Feature Profiling – guides users through annotating protein families and analyzing features across a set of genomes for comparative analysis

Video Tutorial

Introduction to Genome Analysis