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” |
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11-12 | Lecture/Practical: “Basic assembly QC stats” |
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13-14.30 | Lecture/Practical: “Contamination in genome assemblies” |
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14.30-16.30 | Coding session: “Biopython for assembly analysis” |
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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.