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 Genomics in KBase: Drafting Isolate Genomes (Short-reads) – 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) – demonstrates how to draft isolate genomes using Oxford Nanoport MinION long-read sequences from quality assessment to assembly and annotation.

Video Tutorials

Introduction to Genome Analysis

Microbial Genomics in KBase (short- and long-read examples)