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Undergraduate Research Assistant, TMU. June 2026 to now.

Research with Prof. E. Harley

The lab edits genes and needs to know whether each edit actually worked. I built the pipeline that checks, straight from raw DNA-sequencing data.

  1. Before

    Checked by hand

    Results were verified by manual inspection, batch by batch.

  2. The pipeline

    Four tools, one run

    Python chaining fastp, SPAdes, BLAST, and minimap2 across 6 experimental batches. Assemblies validated at 99.8% accuracy.

  3. What it found

    The edit had silently failed

    I traced an unintended copy elsewhere in the genome, and the lab redirected its next round of experiments.

ReadsIntended site, edit not thereUnintended copy,found elsewhere in the genome
Schematic, not real data.
  • 01fastp Read cleanup
  • 02SPAdes Assembly
  • 03BLAST Sequence search
  • 04minimap2 Alignment