Repositories list

• emu

  Public
  Python

  •

  MIT License

  •9•57•9•2•Updated Jul 25, 2025Jul 25, 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•24•2•0•Updated Jul 23, 2025Jul 23, 2025

• omi-command-base

  Public
  Command mode setup instructions to interface with the omi-web-app here (https://github.com/ppreshant/omi-web-app

  Python

  •0•0•1•0•Updated May 23, 2025May 23, 2025

• magnet

  Public
  Jupyter Notebook

  •0•10•4•1•Updated May 22, 2025May 22, 2025

• 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

  •2•28•10•0•Updated May 12, 2025May 12, 2025

• treangenlab.github.io

  Public
  Treangen lab website

  HTML

  •

  MIT License

  •0•0•0•0•Updated May 10, 2025May 10, 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

  •2•48•12•2•Updated Mar 5, 2025Mar 5, 2025

• sampling-scheme-analysis

  Public
  Jupyter Notebook

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

• Mimic

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

  Python

  •

  MIT License

  •1•1•0•0•Updated Dec 19, 2024Dec 19, 2024

• InfA-amplicon

  Public
  Amplicon sequencing of influenza A

  influenzaamplicon-sequencing

  GNU General Public License v3.0

  •0•2•0•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

• rhea

  Public
  Recognizing HGT Events in Assemblies

  Python

  •

  MIT License

  •0•9•1•0•Updated Jan 30, 2024Jan 30, 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 Bruijn graphs) and relies on k-core and K-truss decomposition algorithms.

  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