Repositories list

• Seqwin

  Public
  Ultrafast identification of signature sequences in microbial genomes

  Python

  •

  GNU General Public License v3.0

  •0•15•2•0•Updated Feb 8, 2026Feb 8, 2026

• bronko

  Public
  Ultra-rapid detection of viral variants directly from sequencing data

  virusesvariant-callingkmer+ 2amplicon-sequencingsequencing-data

  Rust

  •

  MIT License

  •0•34•0•0•Updated Feb 6, 2026Feb 6, 2026

• emu

  Public
  Python

  •

  MIT License

  •12•79•6•2•Updated Feb 6, 2026Feb 6, 2026

• treangenlab.github.io

  Public

  treangenlab/treangenlab.github.io’s past year of commit activity
  Treangen lab website

  HTML

  •

  MIT License

  •0•0•0•0•Updated Feb 4, 2026Feb 4, 2026

• Mimic

  Public
  Generates simulated ONT/PacBio metegenomic samples based off real microbiome sample abundances

  Python

  •

  MIT License

  •1•1•0•0•Updated Jan 30, 2026Jan 30, 2026

• Olivar

  Public
  Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens

  bioinformaticsamplicon-sequencing

  Python

  •

  GNU General Public License v3.0

  •3•37•9•0•Updated Jan 22, 2026Jan 22, 2026

• Strainify

  Public
  Abundance analysis tool for short-read metagenomics

  Python

  •

  MIT License

  •0•11•2•0•Updated Dec 2, 2025Dec 2, 2025

• magnet

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•10•4•0•Updated Nov 24, 2025Nov 24, 2025

• bronko-test

  Public
  Analyses and supporting scripts for bronko manuscript

  MIT License

  •0•0•0•0•Updated Nov 20, 2025Nov 20, 2025

• rhea

  Public
  Recognizing HGT Events in Assemblies

  Python

  •

  MIT License

  •0•9•1•0•Updated Sep 29, 2025Sep 29, 2025

• lemur

  Public
  Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets

  metagenomicsmetagenomic-analysismetagenomic-classification+ 4long-readstaxonomic-classificationlong-read-sequencingtaxonomic-profiling

  Python

  •

  MIT License

  •1•25•4•0•Updated Jul 23, 2025Jul 23, 2025

• gut-microbiome-dl

  Public
  Jupyter Notebook

  •0•0•0•0•Updated May 3, 2025May 3, 2025

• radmicrobes

  Public
  2025 RAD microbes boot camp

  HTML

  •

  MIT License

  •3•14•0•1•Updated Apr 30, 2025Apr 30, 2025

• methphaser

  Public
  MethPhaser: methylation-based haplotype phasing of human genomes

  methylationbioinformatics-toolhaplotype-blocks

  Python

  •

  MIT License

  •5•53•12•2•Updated Mar 5, 2025Mar 5, 2025

• sampling-scheme-analysis

  Public
  Jupyter Notebook

  •0•2•0•0•Updated Feb 8, 2025Feb 8, 2025

• InfA-amplicon

  Public
  Amplicon sequencing of influenza A

  influenzaamplicon-sequencing

  GNU General Public License v3.0

  •0•3•1•0•Updated Sep 16, 2024Sep 16, 2024

• crykey_analysis_scripts

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Apr 2, 2024Apr 2, 2024

• wasterwater_arg_metagenomics

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Feb 8, 2024Feb 8, 2024

• crykey

  Public
  Python

  •

  MIT License

  •0•8•1•0•Updated Nov 20, 2023Nov 20, 2023

• komb

  Public
  KOMB is a tool for fast identification of unitigs of interest in metagenomes. KOMB introduces the concept of a Hybrid Unitig Graph (an extension to compacted de…

  metagenomicsmetagenomic-analysisanomaly-detection+ 3metagenomic-pipelinek-core-decompositionshort-read-sequencing

  C++

  •

  GNU General Public License v2.0

  •0•6•1•1•Updated Sep 28, 2023Sep 28, 2023