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Achukwunta/README.md

Hi šŸ‘‹, I'm Augustine Chukwunta

M.Sc. Bioinformatics @ Brandon University

I develop computational workflows to solve agricultural and genomic challenges. My work spans from host-pathogen transcriptomics to metagenomic community profiling and automated pipeline engineering.

šŸ§¬ Technical Focus

  • Transcriptomics: Dual RNA-seq (host-pathogen), de novo assembly, and differential expression analysis.
  • Metagenomics: Microbiome diversity (Alpha/Beta) and taxonomic profiling in plant-soil interfaces.
  • Genomics & Dev: Snakemake workflow development, germline variant calling, and HPC data management.

šŸ”§ My Toolkit

  • Languages: Python, R, Bash, SQL
  • Environment & Workflow: Snakemake, Conda, Git, WSL2 (Ubuntu)

Bioinformatics Toolkit:

  • RNA-Seq & Transcriptomics: HISAT2, Salmon, Trinity, PyDESeq2, FeatureCounts, Trimmomatic, fastp, FastQC, MultiQC
  • DNA-Seq & Variant Calling: GATK (HaplotypeCaller), BWA, SAMtools, Picard, bcftools, SnpEff
  • Microbial Profiling & Annotation: QIIME2, TransDecoder, eggNOG-mapper, BLAST, g:Profiler, DAVID
  • Data Science & Visualization: Pandas, NumPy, Scikit-learn, Matplotlib, Seaborn
  • Databases: NCBI, Ensembl, SoyBase, Phytozome, GEO, VectorBase

šŸš§ Featured Projects

  1. Workflow Engineering: Reproducible germline variant calling pipeline, demonstrated on chr20 using NA12878 raw dataset
  2. De novo Assembly: Transcriptome and comparative analysis of Hypnoidus abbreviatus
  3. Plant-Pathogen Interaction: Dual RNA-seq analysis of Glycine max vs. A. alternata
  4. Microbiome Diversity: Impact of fungicides on Barley rhizosphere and phyllosphere.

Repositories contain pipelines for Dual RNA-seq analysis, de novo assembly, and variant calling. Microbiome repository will be created upon completion.

šŸ“œ Certifications & Professional Development

achukwunta

  • šŸ‘Æ Iā€™m looking to collaborate on Bioinformatics and Data Science projects

  • āš” Fun fact: hiking and gardening

Connect with me:

LinkedIn Profile Email Me

Languages and Tools:

bash linux pandas python scikit_learn seaborn sqlite

achukwunta

Ā achukwunta

Pinned Loading

  1. soybean-alt-rnaseq soybean-alt-rnaseq Public

    Dual RNA-seq analysis of soybean and Alternaria alternata

    Jupyter Notebook

  2. wireworm-transcriptomics wireworm-transcriptomics Public

    De novo assembly and Comparative Analysis of Hypnoidus abbreviatus

    Jupyter Notebook

  3. germline-variant-calling germline-variant-calling Public

    human germline variant calling and variant annotation (GRCh38)

    Shell

āš”