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paribytes/README.md

Hi, I'm Priyanshi - a computational biologist working at the intersection of genomics, machine learning, and clinical impact.

I'm currently at the Sethuraman Lab at SDSU, where I work on genome assembly and annotation for hops (Humulus lupulus) and large-scale NGS pipeline development. Past projects include a telomere biomarker classifier across 8,500+ cancer samples (TCGA) and a population-scale telomere length pipeline across 2,300+ whole genomes from the 1000 Genomes Project. I've also built out an HPC assembly pipeline (MaSuRCA + RagTag) for hop genomes, working through real-world constraints like memory-limited scaffolding steps and cluster-specific dependency issues.

🛠️ My stack: Python · R · Bash · Snakemake · Nextflow · HPC (SLURM/PBS) · AWS · scikit-learn

📄 Publications:

  • Shah & Sethuraman. Biology Methods and Protocols, 2025
  • Shah & Sethuraman. bioRxiv, 2025 (under review)

💼 Open to bioinformatics scientist and computational biology roles with direct clinical impact

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  1. TeloTales TeloTales Public

    Reproducible bioinformatics pipeline for estimating telomere content from whole-genome sequencing (WGS) data from the 1000 Genomes Project.

    Python 1

  2. TeloQuest TeloQuest Public

    Reproducible machine learning pipeline for predicting tumor status from telomere content variation and genomic variants, using whole-genome sequencing (BAM) data from The Cancer Genome Atlas (TCGA).

    Jupyter Notebook 2

  3. julian-gold-hops-assembly julian-gold-hops-assembly Public

    De novo genome assembly (MaSuRCA), reference-guided scaffolding (RagTag), and QC (QUAST, BUSCO, synteny analysis) for Humulus lupulus cv. Julian Gold

    Shell 2

  4. hops-ploidy-analysis hops-ploidy-analysis Public

    K-mer based ploidy estimation for Humulus lupulus samples using KMC and GenomeScope2

    Shell 1