Software
I develop and maintain open-source command-line tools primarily in Rust for performance and reliability, and in R and Python for statistical and analytical workflows. All tools are freely available on GitHub.
Taxonomy and Genomics
xgt ·
Efficient command-line tool for querying and parsing taxonomic data from the Genome Taxonomy Database (GTDB). Supports full taxonomy lookup, lineage tracing, taxon comparison across releases, and bulk queries via the GTDB REST API. Designed for speed on large-scale genomic datasets.
HMM-based tool for identifying and extracting housekeeping genes from prokaryotic genomes and metagenomes. Built for use in both isolate genomics and metagenomics-first workflows, where reliable single-copy marker genes are needed for normalization or phylogenetic anchoring.
cedar ·
Rapid neighbor-joining phylogenetic tree construction directly from sequences, using Mash distance estimation. Designed for quick exploratory phylogenetics on large sequence sets without requiring a full alignment step.
Amplicon Sequencing
hyperex ·
Primer-based extractor for hypervariable regions of 16S rRNA and other SSU/LSU marker genes. Useful for standardizing amplicon datasets across studies that targeted different variable regions, or for in silico primer evaluation.
sabreur ·
Fast and reliable demultiplexing of FASTX files based on barcode sequences. A modern, maintained alternative to the original SABRE, with improved error handling and performance on large sequencing runs.
Statistical Modeling
R packages and modeling frameworks
I am currently developing R packages implementing Bayesian ecological modeling frameworks, with a focus on microbial community analysis, prior sensitivity analysis, and model comparison workflows built around Stan and CmdStanR. These projects will be made public in the coming months.
If you use any of these tools in your work, feedback and contributions are welcome via GitHub. For questions or collaboration inquiries, feel free to get in touch.