Research Object Crate for AmpSeeker

Original URL: https://workflowhub.eu/workflows/1729/ro_crate?version=1

**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](https://sanjaynagi.github.io/AmpSeeker/) 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](https://github.com/features/actions). ## Contributing to AmpSeeker 1. Fork the repository to your own GitHub user account 2. Clone your fork 3. Create a branch to implement the changes or features you would like `git checkout -b my_new_feature-24-03-23` 4. Implement the changes 5. Use `git add FILES`, `git commit -m COMMENT`, and `git push` to push your changes back to the branch 6. Open a Pull request to the main repository 7. 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 git@github.com:sanjaynagi/AmpSeeker.git`. 8. 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!

Author

License

CC-BY-4.0

Contents