Automated indel-based primer design for QTL fine mapping
Project description
IndelPrimerMapper
IndelPrimerMapper is an automated pipeline for indel-based marker development and QTL fine mapping in recombinant plant populations (e.g. F2:3).
Features
- Indel extraction from VCF / CSV
- Primer design using Primer3
- Genome-wide specificity validation using BLAST
- Visualization of recombinant vs non-recombinant gel patterns
Installation
pip install indelprimermapper
Usage
indelprimermapper --variants variants.csv \
--reference genome.fa \
--blast-db genome_db \
--out primers.xlsx
Citation
See CITATION.cff
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