Skip to content
Change the repository type filter

All

    Repositories list

    • CAT_pack

      Public
      CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes
      Python
      MIT License
      35229574Updated Apr 1, 2026Apr 1, 2026
    • This repository contains code and data relative to paper "High throughput genomic feature extraction reveals prokaryotic adaptations to the abiotic environment"…
      Jupyter Notebook
      GNU General Public License v3.0
      0000Updated Mar 25, 2026Mar 25, 2026
    • FxTractor

      Public
      FxTractor is a high-throughput snakemake pipeline to extract features from prokaryotic genomes.
      Python
      GNU General Public License v3.0
      1300Updated Mar 13, 2026Mar 13, 2026
    • Jaeger

      Public
      Jaeger is a quick and precise tool for detecting phages in sequence assemblies.
      Python
      MIT License
      1910Updated Jan 22, 2026Jan 22, 2026
    • Metabolomics analysis with LC-HRMS
      R
      MIT License
      1400Updated Jan 16, 2026Jan 16, 2026
    • This repository contains a tutorial and scripts to create a gene synteny and homology figure for a set of species.
      Jupyter Notebook
      GNU General Public License v3.0
      0800Updated Jan 2, 2026Jan 2, 2026
    • HTML
      Other
      0000Updated Sep 8, 2025Sep 8, 2025
    • HTML
      0000Updated Sep 5, 2025Sep 5, 2025
    • viral ecology along gradient across biomes
      Python
      0201Updated Aug 20, 2025Aug 20, 2025
    • DNNGIOR

      Public
      Scripts to build high-quality genome-scale metabolic model by using a deep neural network to guide gapfilling
      Python
      MIT License
      41981Updated Mar 18, 2025Mar 18, 2025
    • CAT results for the ICTV taxonomy challenge
      Python
      0000Updated Feb 28, 2025Feb 28, 2025
    • Viromics2024

      Public template
      HTML
      Other
      1100Updated Oct 7, 2024Oct 7, 2024
    • Graphite

      Public
      LMEMs in compacted colored De Bruijn graphs
      C
      3410Updated Aug 2, 2024Aug 2, 2024
    • subgraphs

      Public
      Rust
      0100Updated Jun 27, 2024Jun 27, 2024
    • Python
      Other
      3000Updated Jun 24, 2024Jun 24, 2024
    • virus identification tools benchmarking
      Python
      0261Updated Mar 28, 2024Mar 28, 2024
    • CAT_dev

      Public
      CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes
      Python
      MIT License
      0500Updated Mar 8, 2024Mar 8, 2024
    • Python
      0000Updated Jul 25, 2023Jul 25, 2023
    • Calculate the Social Niche Breadth (SNB) score of all taxonomic lineages in a set of microbiomes.
      Python
      MIT License
      1910Updated Apr 13, 2023Apr 13, 2023
    • Python
      Other
      3900Updated Mar 8, 2022Mar 8, 2022
    • phap

      Public
      A snakemake workflow wrapping various phage host prediction tools
      Python
      MIT License
      0130Updated Mar 7, 2022Mar 7, 2022
    • Run metagenomic read classifiers on your input
      Python
      0000Updated Dec 9, 2021Dec 9, 2021
    • cirtap

      Public
      A command line utility for handling data from the PATRIC ftp site
      Python
      MIT License
      0110Updated Nov 24, 2021Nov 24, 2021
    • A proof-of-concept, automated and reproducible pipeline for predicting functional associations between pVOGs.
      Python
      MIT License
      0300Updated Nov 3, 2021Nov 3, 2021
    • 1000Updated Sep 24, 2021Sep 24, 2021
    • gtdb2cat

      Public
      Prototypes for creating a CAT db for GTDB data
      Jupyter Notebook
      MIT License
      0010Updated Aug 2, 2021Aug 2, 2021
    • Treemaker

      Public
      Python
      0000Updated Jun 16, 2021Jun 16, 2021
    • Benchmarking and assembly
      Python
      0000Updated Jun 4, 2021Jun 4, 2021
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.