Quality control and decontamination: practical
Trainer: Jennifer Lu and Varsha Kale
Overview: On this practical your are encouraged to perform quality control on some examples of short read metagenomic data using the concepts discussed in the previous session. You can then visualise quality statistics, filter reads or contigs and understand the importance of experimental controls.
Learning outcomes:
After this session you should be able to:
- Assess the quality of short read sequences, identify adaptor sequences, remove adapters and low-quality sequences, and construct a reference database for host decontamination.
- Generate a PhiX blast database and run a blast search with a subset of assembled freshwater sediment metagenomic reads to identify contamination.
Materials: