{"id":46405182,"url":"https://github.com/mateomics/babesia_genomic_analysis","last_synced_at":"2026-03-05T12:02:16.140Z","repository":{"id":311816896,"uuid":"1045179088","full_name":"mateomics/babesia_genomic_analysis","owner":"mateomics","description":"Proyecto de BioPython, Sem3, LCG. 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This project reproduces and extends the analysis from González et al. (2019) through RNA-seq differential expression analysis.\n\n## Authors\n\n- Héctor López Ordaz \u003chectorjl@lcg.unam.mx\u003e\n- Ismael Maximiliano De Los Santos Huesca \u003cismadlsh@lcg.unam.mx\u003e\n- Mateo Jiménez Sotelo \u003cmajiso@lcg.unam.mx\u003e\n\n## Project Overview\n\nBabesiosis is an emerging zoonotic disease caused by the protozoan parasite *Babesia divergens*, whose incidence has increased significantly over the last 30 years. This project analyzes gene expression patterns associated with invasion and egress processes using a comprehensive bioinformatics pipeline.\n\n## Data Sources\n\n- **RNA-seq Data**:\n  \n  [ID 552284 - BioProject PRJNA552284 - NCBI](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA552284)\n\n  [SRR9624157: NCBI](https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser\u0026acc=SRR9624157\u0026display=download)\n\n  [SRR9624156: NCBI](https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser\u0026acc=SRR9624156\u0026display=download)\n\n  [SRR9624155: NCBI](https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser\u0026acc=SRR9624155\u0026display=download) \n\n  [SRR9624154: NCBI](https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser\u0026acc=SRR9624154\u0026display=metadata)\n\n  [SRR9624153: NCBI](https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser\u0026acc=SRR9624153\u0026display=download)\n\n  [SRR9624152: NCBI](https://trace.ncbi.nlm.nih.gov/Traces/?run=SRR9624152)\n\n- **Reference Genome**: [Datasets NCBI](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/077/455/GCA_001077455.2_ASM107745v2/)\n- **Original Study**: González LM, et al. (2019) PLoS Negl Trop Dis 13(8): e0007680\n\n## Project Structure\n\nbabesia_genomic_analysis/  \n├── bin/ # Executable scripts  \n├── data/ # Raw and processed data\n├── docs/ # Documentation  \n│ ├──Comparative_and_functional_genomics_of_the_protozoan_Babesia_divergens_highlighting_the_invasion_and_egress_processes.pdf  \n│ └── Project_Description_Babesia.md\n├── results/ # Analysis results  \n├── src/ # Source code  \n├── lib/ # Libraries and dependencies  \n├── test/ # Test files  \n├── LICENSE  \n└── README.md\n\n\n## Analysis Pipeline\n\n1.  **Data Acquisition**: Download FASTQ files and reference genome from NCBI\n2.  **Quality Control**: FastQC and MultiQC for read quality assessment\n3.  **Alignment**: HISAT2 alignment to *B. divergens* genome\n4.  **Quantification**: featureCounts for read counting\n5.  **Differential Expression**: DESeq2/edgeR analysis\n6.  **Functional Annotation**: BLAST analysis of DEGs\n7.  **Validation**: Comparison with original study results\n\n## Installation and Usage\n\n[*Installation instructions and usage examples will be added here as the project develops*]\nDue to *GitHub*'s 2Gb quote and genome sizes, which exceded it, we were not able to upload the different *Babesia* `fna` files to the repository, even though they were compressed on a `gz` format. Therefore, they are available using file transfer protocol in the following links:\n- [*Babesia divergens*](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/077/455/GCA_001077455.2_ASM107745v2/GCA_001077455.2_ASM107745v2_genomic.fna.gz)\n- [*Babesia microti*](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/691/945/GCF_000691945.2_ASM69194v2/GCF_000691945.2_ASM69194v2_genomic.fna.gz)\n- [*Babesia bovi*](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/165/395/GCF_000165395.2_ASM16539v2/GCF_000165395.2_ASM16539v2_genomic.fna.gz)\n\n## Expected Results\n\n- Gene expression matrix of *B. divergens*\n- Identification of differentially expressed genes between free and intracellular merozoites\n- Functional annotation of invasion and egress-related genes\n- Validation of original study findings\n- Reproducible analysis pipeline\n\n## Terms of Use\n\nThis project is available under the MIT license. See the LICENSE file for more details.\n\n## Citation\n\nIf you use this work in your research, please cite:  \nLópez Ordaz H, De Los Santos Huesca IM, Jiménez Sotelo M. (2025). Comparative and functional genomics of Babesia divergens highlighting the invasion and egress processes. [GitHub Repository]. https://github.com/mateomics/babesia_genomic_analysis\n\n## Contact\n\nFor questions or issues regarding this project, please open an issue in this repository or contact:\n- Héctor López Ordaz: hectorjl@lcg.unam.mx\n- Ismael Maximiliano De Los Santos Huesca: ismadlsh@lcg.unam.mx\n- Mateo Jiménez Sotelo: majiso@lcg.unam.mx\n\n## References\n\nGonzález LM, Estrada K, Grande R, et al. (2019) Comparative and functional genomics of the protozoan parasite Babesia divergens highlighting the invasion and egress processes. PLoS Negl Trop Dis 13(8): e0007680. https://doi.org/10.1371/journal.pntd.0007680\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmateomics%2Fbabesia_genomic_analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmateomics%2Fbabesia_genomic_analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmateomics%2Fbabesia_genomic_analysis/lists"}