Automated pipeline for Genotyping-by-Sequencing (GBS) analysis in polyploids using TASSEL-4-Poly.
This pipeline, written in Shell and Perl, processes raw sequencing data (FASTQ) all the way to variant calling (VCF).
It includes steps for demultiplexing, tag counting, building intermediate files (TBT, tagCounts, topm), and running TASSEL-4-Poly, producing reproducible results with detailed logs.
- Linux/Unix system
- Java (>= 1.8)
- Perl
- TASSEL-4-Poly
- FASTQ files of genotypes
- Barcode file
- Reference genome (FASTA)
# Clone the repository
git clone https://github.com/pahenrique02/GBS_Tasse4Poly.git
cd GBS_Tasse4Poly
# Make the pipeline executable
chmod +x GBS_Pipeline.sh