Geno Scan

Objective: Analyze your own wheat varieties for CNVb markers and perform variety identification.

1. Choose "Geno Scan" from the main menu.

2. Submit the CNVb file obtained through the aforementioned CNVb scanning process.

3. After submitting, wait for 1-2 minutes, and the page will display the CNVb fingerprint of the wheat variety.

4. Compare your CNVb fingerprint with existing varieties in the database.

Help Documentation of CNVb Pre-Analysis

The WheatCNVb database offers a powerful tool for researchers to identify wheat varieties and compare them with existing accessions by analyzing Copy Number Variation blocks (CNVb). To facilitate this analysis, users must preprocess their genomic data and upload it in a specific format. This document provides a step-by-step guide for preparing your data for the WheatCNVb database.

Step 1: Low-Coverage Sequencing

To identify CNVb fingerprints for your wheat varieties, start with low-coverage sequencing. A minimum coverage of 0.05x (~1GB) is required. This approach ensures that sufficient data is captured for accurate CNVb identification while keeping sequencing costs low.

Step 2: Aligning Sequencing Data to the Pan-Genome Reference

After obtaining the fasta format sequencing data, download the reference pan-genome sequence from WheatPanGenome. Use your preferred bioinformatics tool to align the fasta format sequencing data of your wheat variety to the reference pan-genome sequence. This process will generate a BAM file, which is a binary format for storing sequence data.

Step 3: Running the CNVb Scanning Script to obtain raw CNVb

After obtaining the BAM file of the wheat variety, download the CNVb scanning script from CNVbQuickScan. This script is designed to analyze the BAM file and identify CNV blocks specific to the variety.

Step 4: Uploading Your CNVb File

Finally, upload the CNVb file to the WheatCNVb database via http://wheat.cau.edu.cn/WheatCNVb/userupload.html. This action will allow you to view the CNVb fingerprint of your variety and compare it with the CNVb profiles of other varieties in the database.

Conclusion

By following these steps, you can effectively utilize the WheatCNVb database to identify and compare wheat varieties based on their CNVb profiles. For further assistance or questions, please contact the WheatCNVb support team at niujx@cau.edu.cn.