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kGWASflow is a Snakemake workflow developed for performing k-mers-based genome-wide association study (GWAS) based on the method developed by Voichek et al. (2020). It performs several pre-GWAS analyses, including read trimming, quality control, and k-mer counting. It implements the kmersGWAS method for performing k-mers-based GWAS. The workflow also provides multiple post-GWAS analysis options, such as mapping k-mers to a reference genome, finding and mapping the source reads for k-mers, assembling source reads of k-mers, and mapping them to a reference genome. kGWASflow is highly customizable and offers users multiple options to choose from depending on the user needs.
kGWASflow increases the accessibility of k-mers based GWAS for users while also allowing for additional expansion and improvement in the future.
kGWASflow workflow steps:
- Preprocessing
- k-mers-based GWAS
- Post-GWAS Analyses
If you use kGWASflow in your research, please cite using the DOI: 10.5281/zenodo.7834410 and the original method paper by Voichek et al. (2020):
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Kivanc Corut. akcorut/kGWASflow: v1.2.3. (2023). https://doi.org/10.5281/zenodo.7916305
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Voichek, Y., Weigel, D. Identifying genetic variants underlying phenotypic variation in plants without complete genomes. Nat Genet 52, 534–540 (2020). https://doi.org/10.1038/s41588-020-0612-7
kGWASflow was developed by Adnan Kivanc Corut .
