Module 2.3a Short-read genome assembly and QC 2024

Theme 2: Sequencing and assembly


2.3: Short-read genom assembly and QC


Time

Activity description

ILOs

10-11

Practical: “Bacterial genome assembly with short reads” 

  • Find and understand software documentation and settings for genome assembly 
  • Generate a de novo bacterial genome assembly from short reads
  • Understand the content of the genome assembly output files

11-12

Lecture/Practical: “Basic assembly QC stats” 

  • Describe the most common stats used for evaluating bacterial genome assemblies
  • Run QUAST on genome assembly files and interpret the report-file

13-14.30

Lecture/Practical: “Contamination in genome assemblies” 

  • Describe how contamination impacts genome assembly
  • Describe how and why the proportion of contamination in a sample and the contaminants genomic closeness to the target organism matters to genome assembly results
  • Identify contaminated genome assemblies based on basic QC parameter from Quast
  • Identify contaminant species using kraken on assemblies

 

14.30-16.30

Coding session: “Biopython for assembly analysis” 

  • Use biopython to write custom scripts for filtering and analysis of genome assembly files

 

 

Details

 

During this session, the trainees will get hands-on experience on how to perform a de novo genome assembly with Illumina data, using the SPAdes assembler. As part of the process, we will explore the software documentation, settings and log-file, in order to continue developing good practice for working with bioinformatic tools. After the trainees have computed some assemblies, we will introduce basic QC stats, and discuss how to run and  interpret a QUAST report file. 

 

After the lunch-break, we will give the trainees hands-on experience on how to identify a contaminated genome assembly, and provide some real data examples of why this is of importance. We will wrap up the day with a coding session, building upon the python coding introduced earlier in the week. We will demonstrate how biopython can be used to extract relevant information from assembly files, but there will also be free time for the trainees to explore coding tasks of their own choice.


Last modified: Monday, 25 March 2024, 12:58 PM