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    28 repositories

    • 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
      •35•229•57•4•Updated Apr 1, 2026Apr 1, 2026

    • abiotic_environment

      Public
      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
      •0•0•0•0•Updated 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
      •1•3•0•0•Updated Mar 13, 2026Mar 13, 2026

    • Jaeger

      Public
      Jaeger is a quick and precise tool for detecting phages in sequence assemblies.
      Python
      •
      MIT License
      •1•9•1•0•Updated Jan 22, 2026Jan 22, 2026

    • MetabSpace

      Public
      Metabolomics analysis with LC-HRMS
      R
      •
      MIT License
      •1•4•0•0•Updated Jan 16, 2026Jan 16, 2026

    • genes_synteny

      Public
      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
      •0•8•0•0•Updated Jan 2, 2026Jan 2, 2026

    • Viromics2025

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Sep 8, 2025Sep 8, 2025

    • coalescence_project

      Public
      HTML
      •0•0•0•0•Updated Sep 5, 2025Sep 5, 2025

    • viral_ecology_pipeline

      Public
      viral ecology along gradient across biomes
      Python
      •0•2•0•1•Updated 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
      •4•19•8•1•Updated Mar 18, 2025Mar 18, 2025

    • ICTV_TaxonomyChallenge_CAT

      Public
      CAT results for the ICTV taxonomy challenge
      Python
      •0•0•0•0•Updated Feb 28, 2025Feb 28, 2025

    • Viromics2024

      Public template
      HTML
      •
      Other
      •1•1•0•0•Updated Oct 7, 2024Oct 7, 2024

    • Graphite

      Public
      LMEMs in compacted colored De Bruijn graphs
      C
      •3•4•1•0•Updated Aug 2, 2024Aug 2, 2024

    • subgraphs

      Public
      Rust
      •0•1•0•0•Updated Jun 27, 2024Jun 27, 2024

    • Viromics2024-forked

      Public
      Python
      •
      Other
      •3•0•0•0•Updated Jun 24, 2024Jun 24, 2024

    • virus_identification_tools_benchmarking

      Public
      virus identification tools benchmarking
      Python
      •0•2•6•1•Updated 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
      •0•5•0•0•Updated Mar 8, 2024Mar 8, 2024

    • rothera_crassvirales

      Public
      Python
      •0•0•0•0•Updated Jul 25, 2023Jul 25, 2023

    • social_niche_breadth_SNB

      Public
      Calculate the Social Niche Breadth (SNB) score of all taxonomic lineages in a set of microbiomes.
      Python
      •
      MIT License
      •1•9•1•0•Updated Apr 13, 2023Apr 13, 2023

    • Viromics-Workshop-MGX

      Public
      bioinformaticsviral-metagenomics
      bioinformaticsviral-metagenomics
      Python
      •
      Other
      •3•9•0•0•Updated Mar 8, 2022Mar 8, 2022

    • phap

      Public
      A snakemake workflow wrapping various phage host prediction tools
      bioinformatics-pipelinephage-host-prediction
      bioinformatics-pipelinephage-host-prediction
      Python
      •
      MIT License
      •0•1•3•0•Updated Mar 7, 2022Mar 7, 2022

    • read_classifiers

      Public
      Run metagenomic read classifiers on your input
      Python
      •0•0•0•0•Updated Dec 9, 2021Dec 9, 2021

    • cirtap

      Public
      A command line utility for handling data from the PATRIC ftp site
      Python
      •
      MIT License
      •0•1•1•0•Updated Nov 24, 2021Nov 24, 2021

    • pvogs_function

      Public
      A proof-of-concept, automated and reproducible pipeline for predicting functional associations between pVOGs.
      machine-learningbioinformatics-pipelinefunction-prediction
      machine-learningbioinformatics-pipelinefunction-predictionbacteriophages
      Python
      •
      MIT License
      •0•3•0•0•Updated Nov 3, 2021Nov 3, 2021

    • Viral-Metagenomics-2021

      Public
      1•0•0•0•Updated Sep 24, 2021Sep 24, 2021

    • gtdb2cat

      Public
      Prototypes for creating a CAT db for GTDB data
      Jupyter Notebook
      •
      MIT License
      •0•0•1•0•Updated Aug 2, 2021Aug 2, 2021

    • Treemaker

      Public
      Python
      •0•0•0•0•Updated Jun 16, 2021Jun 16, 2021

    • benchmark_assembly

      Public
      Benchmarking and assembly
      Python
      •0•0•0•0•Updated Jun 4, 2021Jun 4, 2021
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