Repositories list

• ARGprofiler

  Public
  A pipeline for for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets

  argprofiler

  HTML

  •

  Apache License 2.0

  •4•25•2•0•Updated Jan 16, 2025Jan 16, 2025

• gs3_acquired_vs_FG

  Public
  HTML

  •

  MIT License

  •0•0•0•0•Updated Jan 15, 2025Jan 15, 2025

• kma

  Public
  C

  •1•5•2•1•Updated Nov 27, 2024Nov 27, 2024

• SpanSeq

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•7•0•0•Updated Nov 20, 2024Nov 20, 2024

• amrlmclustering

  Public
  0•0•0•0•Updated Sep 13, 2024Sep 13, 2024

• CGPhylo

  Public
  Core Genome Phylogenetics Tool

  Python

  •0•1•0•0•Updated Sep 12, 2024Sep 12, 2024

• KMADBInspector

  Public
  Tool for inspecting a KMA database and fetching stats related to homology of an input sample.

  Python

  •0•0•0•0•Updated Aug 14, 2024Aug 14, 2024

• NanoMGT

  Public
  NanoMarkerGeneTyper

  Python

  •0•0•0•0•Updated Jul 10, 2024Jul 10, 2024

• ccphylo

  Public
  C

  •

  Other

  •0•2•1•0•Updated Jun 27, 2024Jun 27, 2024

• probmap

  Public
  Probabilistic mapper

  Rust

  •0•0•0•0•Updated Jun 6, 2024Jun 6, 2024

• queue_decongestinator

  Public
  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Jun 3, 2024Jun 3, 2024

• functional_testing

  Public
  Python

  •0•0•0•0•Updated Mar 23, 2024Mar 23, 2024

• ListPred

  Public
  Python

  •

  Other

  •1•0•0•0•Updated Mar 1, 2024Mar 1, 2024

• CGELabs

  Public
  CGELabs application for Great Life

  JavaScript

  •1•0•1•0•Updated Feb 25, 2024Feb 25, 2024

• great-life

  Public
  Guide to laptops and ONT software for the great-life project

  Python

  •0•0•0•0•Updated Feb 25, 2024Feb 25, 2024

• cgevirus

  Public
  Virus analysis cge

  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Jan 11, 2024Jan 11, 2024

• cgemetagenomics

  Public
  CGE metagenomics pipeline

  Python

  •

  Apache License 2.0

  •1•1•0•0•Updated Jan 11, 2024Jan 11, 2024

• cgeisolate

  Public
  CGE isolate pipeline

  Python

  •

  Apache License 2.0

  •2•0•0•0•Updated Jan 11, 2024Jan 11, 2024

• cgeutil

  Public
  Generel utility tool for the Great Life Project

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 3, 2024Jan 3, 2024

• argprofiler-paper-notebooks

  Public
  Supporting notebooks for the ARGprofiler manuscript

  argprofiler

  Jupyter Notebook

  •5•2•0•0•Updated Dec 11, 2023Dec 11, 2023

• resfinder

  Public
  Python

  •

  Other

  •1•4•1•0•Updated Nov 23, 2023Nov 23, 2023

• kgt_mlst

  Public
  kmergenetyper mlst parser

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 21, 2023Nov 21, 2023

• outbreak_maker

  Public
  Outbreak_maker

  Python

  •0•0•0•0•Updated Nov 6, 2023Nov 6, 2023

• plasmidfinder

  Public
  Python

  •3•7•2•0•Updated Nov 2, 2023Nov 2, 2023

• cgecore

  Public
  Python

  •0•0•0•0•Updated Oct 30, 2023Oct 30, 2023

• pbs-torque-queue-considerate

  Public
  Python

  •

  MIT License

  •22•0•0•0•Updated Oct 20, 2023Oct 20, 2023

• fqgrep

  Public
  C

  •0•0•0•0•Updated Oct 3, 2023Oct 3, 2023

• fingerseq

  Public
  C

  •0•0•0•0•Updated Oct 3, 2023Oct 3, 2023

• flankophile

  Public
  Python

  •0•3•0•0•Updated Sep 25, 2023Sep 25, 2023

• kmergenetyper

  Public
  Accurate Gene Typer

  Python

  •

  Apache License 2.0

  •0•0•0•1•Updated Sep 18, 2023Sep 18, 2023