Bacterial population genetics

Pathogen Informatics and Modelling @ EMBL-EBI / Bacterial Evolutionary Epidemiology Group @ Imperial College London

United Kingdom

Pinned Repositories

CELEBRIMBOR
Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
Language:Python10 0 20
ggCaller
Bifrost graph gene caller.
Language:C++85 3 276
mandrake
Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
Language:Python36 6 232
PopPIPE
Population analysis PIPEline 🛠🧬
Language:Python12 2 74
PopPUNK
PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
Language:Python86 6 20917
pp-sketchlib
Library of sketching functions used by PopPUNK
Language:C++30 3 517
ska.rust
Split k-mer analysis – version 2
Language:Rust56 4 344
SKA2
Split Kmer Analysis - version 2
Language:C++3 2 90
unitig-caller
Methods to determine sequence element (unitig) presence/absence
Language:Python18 2 233
unitig-counter
Uses cDBG to count unitigs in bacterial populations
Language:C++132

Bacterial population genetics's Repositories

bacpop/PopPUNK
PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
Language:Python86 6 20917
bacpop/ggCaller
Bifrost graph gene caller.
Language:C++85 3 276
bacpop/ska.rust
Split k-mer analysis – version 2
Language:Rust56 4 344
bacpop/mandrake
Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
Language:Python36 6 232
bacpop/pp-sketchlib
Library of sketching functions used by PopPUNK
Language:C++30 3 517
bacpop/unitig-caller
Methods to determine sequence element (unitig) presence/absence
Language:Python18 2 233
bacpop/unitig-counter
Uses cDBG to count unitigs in bacterial populations
Language:C++132
bacpop/PopPIPE
Population analysis PIPEline 🛠🧬
Language:Python12 2 74
bacpop/CELEBRIMBOR
Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs
Language:Python10 0 20
bacpop/cgt
Calculate sensible core gene thresholds for metagenomic data
Language:Rust3
bacpop/SKA2
Split Kmer Analysis - version 2
Language:C++3 2 90
bacpop/CELEBRIMBOR_stan
Language:Stan2
bacpop/Pansim
Pangenome simulator
Language:Rust2
bacpop/sketchlib.rust
Rust reimplementation of pp-sketchlib
Language:Rust21
bacpop/TOMBOMBADIL
Tree-free Omega Mapping By Observing Mutations of Bases and Amino acids Distributed Inside Loci
Language:Stan20
bacpop/BacQuerya
Search engine for bacterial genomic information.
Language:JavaScript1 1 80
bacpop/beebop
Frontend code for beebop
Language:CSS1 1 1
bacpop/ska_simulations
Mutation simulation to test ska.rust sensitivity
Language:Rust1
bacpop/trees_rs
Tree inference in rust
Language:Rust1
bacpop/BacQuerya-api
Backend API for the BacQuerya web app.
Language:Python0 1 20
bacpop/bacpop-website
Code for group website
Language:HTML4
bacpop/Bacquerya-LLM
This repo is for to summarise pubmed texts with a given gene/species query
Language:Python
bacpop/beebop-deploy
Deploy scripts for beebop
Language:Python
bacpop/beebop_py
Python API for beebop
Language:Python0 0
bacpop/compartmental-models-odin-dust
A collection of models that can be implemented, simulated and fitted using odin, dust and mcstate.
Language:HTML
bacpop/DATACIN
Draw A Tree And Colour it IN
Language:Rust1
bacpop/genesearch
bacpop/pp-netlib
Network tools for PopPUNK
Language:Python1 15
bacpop/SBMLtoOdin
An R package for translating SBML models into odin models.
Language:R
bacpop/SimEvoNN
Neural Network modelling for Fisher - Wright Simulation of Evolution
Language:Jupyter Notebook