Repositories list

• Seqwin

  Public
  Ultrafast identification of signature sequences in microbial genomes

  pathogen-detectionmicrobial-specieswastewater-surveillance+ 2

  pathogen-detectionmicrobial-specieswastewater-surveillancesignature-sequenceassay-design

  C++

  •

  GNU General Public License v3.0

  •11 fork•1616 stars•22 issues•11 pull request•Updated May 1, 2026May 1, 2026

• somatem

  Public
  LLM accessible long-read metagenomics pipeline with best practices

  Nextflow

  •

  GNU General Public License v3.0

  •00 forks•11 star•2727 issues•11 pull request•Updated Apr 30, 2026Apr 30, 2026

• somatem-docs

  Public
  documents of the pipeline: flowchart, tools list, etc. in structured human readable formats

  Mermaid

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 30, 2026Apr 30, 2026

• lemur

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

  metagenomicsmetagenomic-analysismetagenomic-classification+ 4

  metagenomicsmetagenomic-analysismetagenomic-classificationlong-readstaxonomic-classificationlong-read-sequencingtaxonomic-profiling

  Python

  •

  MIT License

  •11 fork•2525 stars•44 issues•11 pull request•Updated Apr 30, 2026Apr 30, 2026

• Strainify

  Public
  Abundance analysis tool for short-read metagenomics

  Python

  •

  MIT License

  •00 forks•1010 stars•22 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• radmicrobes

  Public
  2025 RAD microbes boot camp

  HTML

  •

  MIT License

  •33 forks•1616 stars•00 issues•11 pull request•Updated Apr 9, 2026Apr 9, 2026

• bronko-test

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• Strainify_paper

  Public
  Scripts to reproduce results in the Strainify manuscript

  Shell

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• Olivar

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

  primer-designamplicon-sequencingsars-cov-2+ 1

  primer-designamplicon-sequencingsars-cov-2tiled-amplicons

  Python

  •

  GNU General Public License v3.0

  •33 forks•3939 stars•88 issues•00 pull requests•Updated Apr 6, 2026Apr 6, 2026

• emu

  Public
  Python

  •

  MIT License

  •1414 forks•8787 stars•77 issues•22 pull requests•Updated Apr 5, 2026Apr 5, 2026

• Kente

  Public
  Python

  •00 forks•33 stars•00 issues•00 pull requests•Updated Mar 13, 2026Mar 13, 2026

• PlasmidScreen

  Public
  Python

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 24, 2026Feb 24, 2026

• bronko

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

  virusesvariant-callingkmer+ 2

  virusesvariant-callingkmeramplicon-sequencingsequencing-data

  Rust

  •

  MIT License

  •00 forks•4040 stars•00 issues•00 pull requests•Updated Feb 17, 2026Feb 17, 2026

• treangenlab.github.io

  Public
  Treangen lab website

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 4, 2026Feb 4, 2026

• Mimic

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

  Python

  •

  MIT License

  •11 fork•11 star•00 issues•00 pull requests•Updated Jan 30, 2026Jan 30, 2026

• magnet

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•1010 stars•44 issues•00 pull requests•Updated Nov 24, 2025Nov 24, 2025

• rhea

  Public
  Recognizing HGT Events in Assemblies

  Python

  •

  MIT License

  •00 forks•1010 stars•11 issue•00 pull requests•Updated Sep 29, 2025Sep 29, 2025

• gut-microbiome-dl

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 3, 2025May 3, 2025

• methphaser

  Public
  MethPhaser: methylation-based haplotype phasing of human genomes

  methylationbioinformatics-toolhaplotype-blocks

  methylationbioinformatics-toolhaplotype-blocks

  Python

  •

  MIT License

  •66 forks•5454 stars•1313 issues•22 pull requests•Updated Mar 5, 2025Mar 5, 2025

• sampling-scheme-analysis

  Public
  Jupyter Notebook

  •00 forks•22 stars•00 issues•00 pull requests•Updated Feb 8, 2025Feb 8, 2025

• InfA-amplicon

  Public
  Amplicon sequencing of influenza A

  influenzaamplicon-sequencing

  influenzaamplicon-sequencing

  GNU General Public License v3.0

  •00 forks•44 stars•11 issue•00 pull requests•Updated Sep 16, 2024Sep 16, 2024

• crykey_analysis_scripts

  Public
  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 2, 2024Apr 2, 2024

• wasterwater_arg_metagenomics

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 8, 2024Feb 8, 2024

• crykey

  Public
  Python

  •

  MIT License

  •00 forks•88 stars•11 issue•00 pull requests•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+ 3

  metagenomicsmetagenomic-analysisanomaly-detectionmetagenomic-pipelinek-core-decompositionshort-read-sequencing

  C++

  •

  GNU General Public License v2.0

  •00 forks•77 stars•11 issue•11 pull request•Updated Sep 28, 2023Sep 28, 2023