- Author: Qionghou Li (liqionghou@njau.edu.cn)
This repository includes the pipeline used for the research presented in the article "Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and genomic basis of fruit quality traits". The study focuses on pear genome assemblies and the construction of a pangenome graph, highlighting allele-specific expressions and a broad set of genetic variations.
Special Note: These codes are for my personal use and may require modifications for your species. Please handle them with caution.
The pipeline encompasses several key processes:
- Reads Partition: Classifying and organizing sequencing reads based on their genomic origin.
- Allelle Identification: Identification allelles from two haplotype genomes.
- Pangenome Construction: Building a pangenome graph based on minigraph-cactus apporach
- Graph-based SNP Calling: Utilizing the pangenome for SNP calling across different pear accessions.
Genomic data (including sequence, GFF, and pangenome graph generated in this manuscript) are available at the Pear Multiomics Database (https://pearomics.njau.edu.cn/).
This project is licensed under the MIT License - see the LICENSE.md file for details.
Please cite this paper if you find our pipeline or script helpful in your study:
Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and genomic basis of fruit quality traits. Plant Communications. https://doi.org/10.1016/j.xplc.2024.101000