Comp Bio enthusiast
Published and in-progress work from academia
- Desmognathus_TE_analysis - 34-species Desmognathus TE evolution — repeat classification, divergence, PGLS, PERMANOVA, BM/OU, LTR age, figures (Python & R).
- Heat_shock_protein_selection_analysis - Master's work on heat-shock protein orthogroup selection across fish lineages.
Dino-tools
- dino-seq - FASTQ/FASTA parser crate for low-allocation Rust sequencing workflows.
- dino-quant - compressed DNA sketch prefilter experiments.
- orbweaver - Compact grammar-derived motif graphs from genomic FASTA; cross-species comparison with bounded memory.
- Raptor - Parallel graph-based RNA-seq assembler (k-mer extension, isoform graphs, optional GPU, HPC workflows).
- motif_graph_explore - Genomic motif complexity via assembly-theory-style analysis. assemblers & motif graphs
- hox-core - Workspace crates (
hox-parse,hox-common,hox-graph,hox-align,hox-olap) for mmap I/O, FM/minimizer indexes, alignment benches, and Arrow/Parquet-oriented outputs. - genome-assembler-graph - Interactive map of modern assembly tools, inputs, outputs, and metrics.
TUI/CLI tools
- opengenome - Local-first terminal app for setting up and running genome workflows.
- BioDex - Terminal species atlas — taxonomy browser, cached research notebook, genome-stat lookup.
- dino-dna - DNA/RNA terminal animations and codon-aware helices.
- SWATCH - Slurm job monitor — real-time status, SSH auth, dark-theme GUI (
pip install swatch-slurm). - bioutil - Workstation bootstrap for fresh Linux installs (conda, tools, paths).
- nf_denovo_transcriptome - Sample sheet → QC → merge → normalize → rnaSPAdes/Trinity → BUSCO.
- nf_BFFcent - Population genomics: read groups → alignment → GVCF → joint calling → PCA.
- Repeatome_builder - Repeat-library assembly for non-model organisms.
- opengenome reference workflow - Nextflow reference-based WGS workflow.
- opengenome VCF report workflow - Nextflow report workflow for existing VCFs.
- opengenome de novo assembly workflow - Nextflow long-read assembly workflow.
- cellprofiler - Salamander brightfield cell/nucleus measurements.
Agentic attempts at ports. These live on GitHub only; the original tools belong to their original authors.
- bowtie2-rs - Bowtie2 port workspace — lane-by-lane parity before aligner/index core.
- bbnorm-rs - BBTools BBNorm-style read-depth normalization.
- Mobile_DNA_Sim - Transposable-element mobility simulation.
- organism-id-genome-stats - Image-based ID plus NCBI genome stats and nearest-sequenced relative fallback.
