Hi, I'm Jake 🦎

Comp Bio enthusiest

Academic research 🧬

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.

Developments and Research🧩

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.

Terminal & HPC utilities 🌿

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).

Sequencing pipelines 🌾

• 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.
• • add the nextflow pipelines here from opengenome as seperate pipelines and repos

Microscopy & labeling 🔬

• cellprofiler - Salamander brightfield cell/nucleus measurements.
• gemma4-sam31-app - Local microscopy review with model-assisted workflows.
• data_labler - Pattern-classification labeling UI.

Rust ports — legacy tools, measured rewrites 🦀

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.

Misc

• Mobile_DNA_Sim - Transposable-element mobility simulation.
• organism-id-genome-stats - Image-based ID plus NCBI genome stats and nearest-sequenced relative fallback.

GitHub activity 🌱

Connect 🌲

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