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Sorghum Pan-Transcriptome Project

This repository contains the files and data related to the construction of the sorghum pan-transcriptome. The project aims to explore the transcriptome of sorghum and analyze its genetic diversity and functional elements.

Project Structure

#The repository is organized into the following folders:

  • assemblies: Contains assembled transcriptome data for different sorghum genotypes.
  • busco: Data and scripts related to BUSCO (Benchmarking Universal Single-Copy Orthologs) analysis.
  • busco_plots: Visualizations and plots generated from BUSCO analysis.
  • distance_based_inflation_eval: Scripts and data for evaluating inflation values based on distance metrics.
  • domain_based_inflation_eval: Scripts and data for evaluating inflation values based on domain annotations.
  • orthofinder: Files and scripts related to OrthoFinder, used for orthogroup inference.
  • PANZZER2: Tools and resources for functional annotation.
  • pantranscriptome: Output files and data related to the constructed sorghum pan-transcriptome.
  • pfam: Data and scripts for Pfam domain analysis.
  • snakemake: Workflow scripts or configuration for Snakemake, a workflow management system.
  • transrate: Data and scripts for transcriptome quality assessment using TransRate.
  • transrate_plot: Visualizations and plots generated from TransRate analysis.
  • transdecoder: Tools and resources for transcriptome CDS and proteins.

Usage

This repository serves as a central location for storing and sharing the code, data, and results of the sorghum pan-transcriptome project. You can browse the directories to access specific files or download the entire repository for further analysis.

License

This project is licensed under the MIT License. Feel free to use the code and data in this repository according to the terms of the license.