A collection of workflows for processing amplicon sequencing data to identify haplotypes and SNPs, enabling efficient genetic variant analysis.
The repository comprises two main branches corresponding to separate pipelines:
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HaplotypR Workflow: based on the publicly-available HaplotypR pipeline. It can be used to reproduce results from previous studies or analyze new data with the same published approach.
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Alignment-Based Workflow: under development, employs an alignment-based approach to analyze amplicon sequencing data, identify SNPs, call haplotypes and includes additional resources to support data analysis for therapeutic efficacy studies.
For further information and tutorials, check the wiki page.