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Bacterial population genetics · GitHub

Bacterial population genetics

Pathogen Informatics and Modelling @ EMBL-EBI

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PopPUNK PopPUNK Public

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

Python 109 22
PopPIPE PopPIPE Public

Population analysis PIPEline 🛠🧬

Python 26 7
sketchlib.rust sketchlib.rust Public

Fast sequence distance estimates

Rust 31 6
ggCaller ggCaller Public

Bifrost graph gene caller.

C++ 100 6
ska.rust ska.rust Public

Split k-mer analysis – version 2

Rust 105 9
sparrowhawk sparrowhawk Public

In-browser tools for bacterial genome analysis 🦅

Vue 11 1

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ALLCAPS Public
Developing AI tools to analyse pneumococcal capsular biosynthetic loci, the primary target of Pneumococcal Conjugate Vaccines (PCVs).

bacpop/ALLCAPS's past year of commit activity

Jupyter Notebook 2 MIT 0 1 1 Updated Aug 28, 2026
ALLCAPS_Benchmark Public

bacpop/ALLCAPS_Benchmark's past year of commit activity

Nextflow 0 0 0 0 Updated Aug 27, 2026
ggCaller Public
Bifrost graph gene caller.

bacpop/ggCaller's past year of commit activity

C++ 100 MIT 6 6 0 Updated Aug 27, 2026
pangenomerge Public

bacpop/pangenomerge's past year of commit activity

Python 5 MIT 3 0 0 Updated Aug 27, 2026
sparrowhawk Public
In-browser tools for bacterial genome analysis 🦅

bacpop/sparrowhawk's past year of commit activity

Vue 11 Apache-2.0 1 4 1 Updated Aug 27, 2026
TOMBOMBADIL_jax Public
JAX prototype of TOMBOMBADIL

bacpop/TOMBOMBADIL_jax's past year of commit activity

Python 0 Apache-2.0 0 0 0 Updated Aug 24, 2026
sketchlib.rust Public
Fast sequence distance estimates

bacpop/sketchlib.rust's past year of commit activity

Rust 31 Apache-2.0 6 16 1 Updated Aug 24, 2026
mandrake.rust Public
rust port of the mandrake (stochastic cluster embedding) algorithm

bacpop/mandrake.rust's past year of commit activity

Rust 1 Apache-2.0 0 0 0 Updated Aug 21, 2026
poppunk.rust Public
rust reimplementation of PopPUNK

bacpop/poppunk.rust's past year of commit activity

Rust 0 Apache-2.0 0 1 0 Updated Aug 21, 2026
sparrowhawk-amr Public
AMR detection, WebAssembly ready, and AMRFinderPlus DB-compatible, on Rust

bacpop/sparrowhawk-amr's past year of commit activity

Rust 0 0 0 0 Updated Aug 10, 2026

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