Day 2: Microbial Genome Assembly (from short and long reads) and Genome Annotation

In this lab we will perform de novo bacterial genome assembly. We will also annotate the assembled genome. Although we will specifically be assembling a Mycobacteria tuberculosis genome, the methodology presented here applies to any bacterial genome.You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will know:

1. How to perform basic quality checks on the read data
2. How to run a short read assembler on Illumina short reads
3. How to run a long read assembler on Pacific Biosciences long reads
4. How to improve the accuracy of a long read assembly using short reads
5. How to assess the quality of an assembly
6. How to annotate a microbial genome

• Data Sets
• Copying data and preparing the directories
• Read Quality Control and Trimming
  • Running fastqc
  • Running sickle to quality trim reads:
• Pre-assembly Quality Control
• Assembly
  • Assembly using Illumina short reads
  • Assembly using PacBio long reads
• Assessing the quality of the assemblies
• Improving the accuracy of the long read assembly
• Microbial Genome Annotation
  • Visualizing the annotations with Artemis