treangenlab repositories

30 repositories

Seqwin
Public
Ultrafast identification of signature sequences in microbial genomes
pathogen-detection microbial-species wastewater-surveillance
pathogen-detection microbial-species wastewater-surveillance signature-sequence assay-design
Python
•
GNU General Public License v3.0
•1•20•1•0•Updated Sep 4, 2026Sep 4, 2026
PlasmidScreen
Public
Python
•
MIT License
•0•1•2•0•Updated Sep 4, 2026Sep 4, 2026
bronko
Public
Ultra-rapid detection of viral variants directly from sequencing data
bioinformatics alignment viruses
bioinformatics alignment viruses variant-calling kmer amplicon-sequencing sequencing-data
Rust
•
MIT License
•0•47•0•0•Updated Aug 31, 2026Aug 31, 2026
mbcausal
Public
causal inference from longitudinal gut microbiome profiles: interpretable NMF factors, an identifiability screen that runs before any effect is fit, and lagged …
metagenomics ibd causal-inference
metagenomics ibd causal-inference nmf
Python
•0•2•0•0•Updated Aug 5, 2026Aug 5, 2026
bakeoff
Public
repository for scripts, figures, and result tables of bakeoff evaluations
Jupyter Notebook
•0•0•0•0•Updated Jul 29, 2026Jul 29, 2026
somatem
Public
LLM accessible long-read metagenomics pipeline with best practices
Python
•
GNU General Public License v3.0
•0•4•10•1•Updated Jul 16, 2026Jul 16, 2026
Strainify
Public
Strain-level abundance analysis tool for short-read metagenomics
Python
•
MIT License
•0•12•2•0•Updated Jul 12, 2026Jul 12, 2026
Mimic
Public
Generates simulated ONT/PacBio metegenomic samples based off real microbiome sample abundances
Python
•
MIT License
•1•2•0•1•Updated May 25, 2026May 25, 2026
mft-tools
Public
Tranform DNA sequences using the Min-Frame Transformation (MFT)
Rust
•
MIT License
•0•3•0•0•Updated May 20, 2026May 20, 2026
mft-analyses
Public
Repository of analyses for mft paper
Jupyter Notebook
•
MIT License
•0•1•0•0•Updated May 20, 2026May 20, 2026
somatem-docs
Public
documents of the pipeline: flowchart, tools list, etc. in structured human readable formats
Mermaid
•
GNU General Public License v3.0
•0•0•0•0•Updated May 16, 2026May 16, 2026
rhea
Public
Recognizing HGT Events in Assemblies
Python
•
MIT License
•0•10•3•1•Updated May 12, 2026May 12, 2026
parsnp_external_mums
Public
C++
•
Other
•29•0•0•0•Updated May 11, 2026May 11, 2026
lemur
Public
Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets
metagenomics metagenomic-analysis metagenomic-classification
metagenomics metagenomic-analysis metagenomic-classification long-reads taxonomic-classification long-read-sequencing taxonomic-profiling
Python
•
MIT License
•1•25•4•1•Updated Apr 30, 2026Apr 30, 2026
radmicrobes
Public
2025 RAD microbes boot camp
HTML
•
MIT License
•3•17•0•1•Updated Apr 9, 2026Apr 9, 2026
bronko-test
Public
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Apr 8, 2026Apr 8, 2026
Strainify_paper
Public
Scripts to reproduce results in the Strainify manuscript
Shell
•
MIT License
•0•0•0•0•Updated Apr 7, 2026Apr 7, 2026
Olivar
Public
Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
primer-design amplicon-sequencing sars-cov-2
primer-design amplicon-sequencing sars-cov-2 tiled-amplicons
Python
•
GNU General Public License v3.0
•3•42•8•0•Updated Apr 6, 2026Apr 6, 2026
emu
Public
Python
•
MIT License
•15•98•11•3•Updated Apr 5, 2026Apr 5, 2026
Kente
Public
Python
•0•4•1•0•Updated Mar 13, 2026Mar 13, 2026
treangenlab.github.io
Public
Treangen lab website
HTML
•
MIT License
•0•0•0•0•Updated Feb 4, 2026Feb 4, 2026
magnet
Public
Jupyter Notebook
•
GNU General Public License v3.0
•0•11•4•0•Updated Nov 24, 2025Nov 24, 2025
gut-microbiome-dl
Public
Jupyter Notebook
•0•0•0•0•Updated May 3, 2025May 3, 2025
methphaser
Public
MethPhaser: methylation-based haplotype phasing of human genomes
methylation bioinformatics-tool haplotype-blocks
methylation bioinformatics-tool haplotype-blocks
Python
•
MIT License
•6•56•14•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
influenza amplicon-sequencing
influenza amplicon-sequencing
GNU General Public License v3.0
•0•4•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…
metagenomics metagenomic-analysis anomaly-detection
metagenomics metagenomic-analysis anomaly-detection metagenomic-pipeline k-core-decomposition short-read-sequencing
C++
•
GNU General Public License v2.0
•0•7•1•1•Updated Sep 28, 2023Sep 28, 2023

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Treangen Lab

All

30 repositories

Seqwin

PlasmidScreen

bronko

mbcausal

bakeoff

somatem

Strainify

Mimic

mft-tools

mft-analyses

somatem-docs

rhea

parsnp_external_mums

lemur

radmicrobes

bronko-test

Strainify_paper

Olivar

emu

Kente

treangenlab.github.io

magnet

gut-microbiome-dl

methphaser

sampling-scheme-analysis

InfA-amplicon

crykey_analysis_scripts

wasterwater_arg_metagenomics

crykey

komb

Repositories list

30 repositories