RNA-seq Transcript Quantification Workflow
Built a reproducible RNA-seq workflow in Snakemake with reference-guided analysis using STAR and featureCounts, plus de novo transcript quantification with Trinity, Kallisto, and RSEM.
Projects .
Computational projects that demonstrate my foundation in genomic data analysis, workflow engineering, reproducibility, and scientific software development as I build toward machine learning research in biology.
Bacterial Genome Assembly & Annotation
Built a Snakemake workflow for bacterial whole-genome sequencing analysis, including QC, short-read or hybrid assembly, polishing, annotation, core-genome phylogeny, and optional MLST, AMR, virulence, and plasmid screening.
RNA-seq Polyadenylated Reads Workflow
Designed and implemented a Nextflow DSL2 workflow to recover RNA-seq reads with visible poly(A)/poly(T) tail signal, trim the tail sequence, and realign the mRNA-derived read body to a reference genome.
Viral Genome Analysis Pipeline
Built a Snakemake pipeline for Human Adenovirus genome assembly, comparative genomics, and phylogenetic analysis, from raw paired-end reads through QC, assembly, scaffolding, consensus calling, variability plots, and tree generation.