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 gene drive and insecticide resistance monitoring. The pipeline is a work in progress, however, it currently implements:

• BCL to Fastq conversion

• Genome alignment

• Variant calling

• Quality control

• Coverage

• Visualisation of reads in IGV

• VCF to DataFrame/.xlsx

• Allele frequency calculation

• Principal component analysis

• Geographic sample maps

• Genetic diversity

• Kdr origin analysis (ag-vampir)

• Species assignment (ag-vampir)

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 wiki for more information on running the workflow. If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and, if available, its DOI (see above).

Testing

Test cases are in the subfolder .test. They are automatically executed via continuous integration with Github 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!