Comp Bio enthusiest
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
- dino-quant
- 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
- BioDex - Terminal species atlas — taxonomy browser, cached research notebook, genome-stat lookup.
- bio-terminal - DNA/RNA matrix rain and codon-aware helices (
cargo install bio-terminal). * this one got its name changed to dino -dna - 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.
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- add the nextflow pipelines here from opengenome as seperate pipelines and repos
- cellprofiler - Salamander brightfield cell/nucleus measurements.
- gemma4-sam31-app - Local microscopy review with model-assisted workflows.
- data_labler - Pattern-classification labeling UI.
Agentic attempts at ports
- spades-rs - SPAdes 4.2.0 rewrite workspace with upstream oracles and staged lane promotion.
- hifiasm-rs - hifiasm / hifiasm-UL stage benchmarks before custom assembler code.
- bowtie2-rs - Bowtie2 port workspace — lane-by-lane parity before aligner/index core.
- bbnorm-rs - BBTools BBNorm-style read-depth normalization.
- bio_format_speed - Reproducible checks for biological file-format overhead.
- Mobile_DNA_Sim - Transposable-element mobility simulation.
- organism-id-genome-stats - Image-based ID plus NCBI genome stats and nearest-sequenced relative fallback.
