AmpSeeker

Documentation: https://sanjaynagi.github.io/AmpSeeker/

AmpSeeker is a snakemake workflow for Amplicon Sequencing data analysis. The pipeline is generic and can work on any data, but is tailored towards insecticide resistance monitoring. It implements:

BCL to Fastq conversion
Genome alignment
Variant calling
Quality control
Coverage
Visualisation of reads in IGV
VCF to DataFrame/.xlsx
Allele frequency calculation
Population structure
Geographic sample maps
Genetic diversity
Kdr origin analysis (Ag-vampIR panel)
Species assignment (Ag-vampIR panel)

The workflow uses a combination of papermill and jupyter book, so that users can visually explore the results in a local webpage for convenience.

Usage

Please see the documentation for more information on running the workflow.

Citation

Targeted genomic surveillance of insecticide resistance in African malaria vectors
Nagi, et al., 2025. bioRxiv. doi: https://doi.org/10.1101/2025.02.14.637727

Testing

Test cases are in the subfolder .test. They are automatically executed via continuous integration with GitHub Actions.

Contributing to AmpSeeker

Fork the repository to your own GitHub user account
Clone your fork
Create a branch to implement the changes or features you would like git checkout -b my_new_feature-24-03-23
Implement the changes
Use git add FILES, git commit -m COMMENT, and git push to push your changes back to the branch
Open a Pull request to the main repository
Once the pull request is merged, either delete your fork, or switch back to the main branch git checkout main and use git pull upstream main to incorporate the changes back in your local repo. Prior to git pull upstream main, you may need to set sanjaynagi/AmpSeeker as the upstream remote url, with git remote set-url upstream [email protected]:sanjaynagi/AmpSeeker.git.
At this stage, your local repo should be up to date with the main Ampseeker branch and you are ready to start from #3 if you have more contributions!

Version History