Transcriptomics, selection and assay design for malaria vector surveillance
This course follows on from the
MalariaGEN–PAMCA training course,
which we assume you have completed (Workshop 1 at minimum). That course teaches population
genomics with whole-genome sequence data and malariagen_data. This course covers the other
data types and tools used in insecticide resistance research: RNA-seq, the selection atlas,
primer and probe design, and amplicon sequencing.
The whole course follows one study. You will be given a few candidate genes on Day 2 and follow them through every later module, from expression data to a field assay. On Day 5 you present what you found. See the study brief.
Learning outcomes¶
By the end of the course you will be able to:
Explain how genomic surveillance can support malaria vector control.
Configure and run bioinformatic workflows (Snakemake), and explain why workflow managers matter.
Analyse RNA-seq and amplicon sequencing data to identify markers associated with insecticide resistance.
Interpret results from RNA-seq, selection scans and amplicon sequencing with confidence.
Design primers, probes and multiplex panels to validate and monitor candidate resistance markers.
Tools¶
| Tool | Used for |
|---|---|
| RNA-Seq-Pop | RNA-seq workflow: expression and variation |
| AnoExpress | Meta-analysis of resistance RNA-seq studies |
| malariagen_data | Ag1000G whole-genome data |
| Selection atlas | Catalogue of selective sweeps |
| AnoPrimer | Primer and probe design |
| multiply | Multiplex PCR design |
| AmpSeeker | Amplicon sequencing workflow |
Running the notebooks¶
Most notebooks run in Google Colab; use the Colab button at the top of each page. The two Snakemake workflows (RNA-Seq-Pop and AmpSeeker) run in GitHub Codespaces. See Day 1, module 1.4 for setup.
Licence¶
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.