Pear_Haplotype_Genome

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Pear_Haplotype_Genome

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Codes for pear haplotype genome and pangenome graph construction

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## Haplotype-resolved T2T Genome Assemblies and Pangenome Graph of Pear

- Author: Qionghou Li (liqionghou@njau.edu.cn)

## Introduction

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.**

## Repository Overview

The pipeline encompasses several key processes:

1. **Reads Partition**: Classifying and organizing sequencing reads based on their genomic origin.
2. **Allelle Identification**: Identification allelles from two haplotype genomes.
3. **Pangenome Construction**: Building a pangenome graph based on minigraph-cactus apporach
4. **Graph-based SNP Calling**: Utilizing the pangenome for SNP calling across different pear accessions.

## Data
**If you cannot access https://pearomics.njau.edu.cn/ to download the genome data, please use the following link instead:**

Download link: https://pan.baidu.com/s/1BRQDj8BfO8Mbz_W0q3W0VA?pwd=btut

Password: btut

Genomic data (including sequence, GFF, and pangenome graph generated in this manuscript) are available at the Pear Multiomics Database (https://pearomics.njau.edu.cn/).

## License

This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details.

## Citation

Please cite this paper if you find our pipeline or script helpful in your study:

<B>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</B>

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