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    31 repositories

    • atlas

      Public
      ATLAS - Three commands to start analyzing your metagenome data
      snakemakeannotationassembly
      snakemakeannotationassemblymetagenomicstaxonomic-classificationsgenomic-binningfunctional-annotation
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •98•404•2•10•Updated Nov 28, 2025Nov 28, 2025

    • metagenome_instrain

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 14, 2025May 14, 2025

    • metagenome-assembly

      Public
      Workflow module for metagenome assembly
      Python
      •
      MIT License
      •0•2•0•0•Updated Jun 25, 2024Jun 25, 2024

    • snakemake-wrappers

      Public
      This is the development home of the Snakemake wrapper repository, see
      CAP CDS
      •210•0•0•1•Updated Jan 15, 2024Jan 15, 2024

    • Tutorial

      Public
      A tutorial for Metagenome-Atlas
      MAXScript
      •
      GNU General Public License v3.0
      •11•23•4•2•Updated Nov 24, 2023Nov 24, 2023

    • genecatalog_atlas

      Public
      Extended genecatalog workflow for metagenome-atlas
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 27, 2023Sep 27, 2023

    • genome-annotator

      Public
      Python
      •
      MIT License
      •0•3•1•0•Updated Sep 27, 2023Sep 27, 2023

    • supp_data_atlas

      Public
      Supplementary data for Atlas manuscript
      Jupyter Notebook
      •1•1•0•0•Updated Sep 27, 2023Sep 27, 2023

    • plasmid_atlas

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 27, 2023Sep 27, 2023

    • kingfisher_workflow

      Public
      This is a workflow that allows you to download whole projects and metadata with kingfisher. Additionally, it takes care about merging same samples together.
      Python
      •
      MIT License
      •1•0•0•0•Updated Aug 31, 2023Aug 31, 2023

    • snake_gtdbtk

      Public
      A snakemake for GTDB-tk
      Python
      •1•6•0•0•Updated Aug 31, 2023Aug 31, 2023

    • virsearch

      Public
      Snakemake workflow to detect and classify viruses in metagenome assemblies.
      Python
      •
      MIT License
      •5•0•0•0•Updated Aug 31, 2023Aug 31, 2023

    • Tryitout

      Public
      Shell
      •0•0•0•0•Updated Jul 5, 2023Jul 5, 2023

    • metagenome-atlas.github.io

      Public
      MIT License
      •0•0•0•0•Updated Mar 22, 2023Mar 22, 2023

    • clusterprofile

      Public
      Snakemake profile for cluster submission of Atlas on almost any cluster system
      Python
      •
      MIT License
      •11•2•0•2•Updated Sep 14, 2022Sep 14, 2022

    • old_atlas_webpage

      Public archive
      📝 Easily create a beautiful website using Academic, Hugo, and Netlify
      Shell
      •
      MIT License
      •6.5k•0•0•0•Updated Apr 6, 2022Apr 6, 2022

    • BinderTutorial

      Public
      This repo contains the environment needed for the Tutorial
      Shell
      •0•0•0•0•Updated Dec 1, 2021Dec 1, 2021

    • genome_atlas

      Public
      Snakefile pipeline for taxonomic and functional annotation of (Metagenome assembled) genome
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 10, 2021Nov 10, 2021

    • snakemake-metagenome-workflows

      Public
      A collection of snakemake-workflows for metagenomics that can be used as modules
      0•1•0•0•Updated Nov 10, 2021Nov 10, 2021

    • Tutorial_Finnland

      Public
      Tutorial given in 2021
      2•5•0•0•Updated Oct 1, 2021Oct 1, 2021

    • staged-recipes

      Public
      A place to submit conda recipes before they become fully fledged conda-forge feedstocks
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5.9k•0•0•0•Updated Sep 2, 2021Sep 2, 2021

    • old_metagenome-atlas.github.io

      Public archive
      Website
      HTML
      •0•0•0•0•Updated Sep 1, 2021Sep 1, 2021

    • atlas_analyze

      Public archive
      Scripts to get the most of the output of metagenome-atlas
      Python
      •1•5•4•0•Updated Mar 17, 2021Mar 17, 2021

    • DRAM

      Public
      Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
      Python
      •
      GNU General Public License v3.0
      •61•0•0•0•Updated Jan 15, 2021Jan 15, 2021

    • function_atlas

      Public
      0•0•0•0•Updated Jan 12, 2021Jan 12, 2021

    • Example

      Public
      This is an example output of metagenome Atlas v2.4
      MAXScript
      •0•0•1•0•Updated Aug 25, 2020Aug 25, 2020

    • Demo

      Public
      Demo of metagenome Atlas
      0•0•0•0•Updated Jun 8, 2020Jun 8, 2020

    • virome_atlas

      Public
      atlas extension for phage discovery
      Python
      •
      MIT License
      •0•1•0•0•Updated Apr 29, 2020Apr 29, 2020

    • quantification_atlas

      Public
      Workflow for quantifications
      Python
      •0•0•0•0•Updated Mar 11, 2020Mar 11, 2020

    • example_data

      Public
      Shell
      •0•0•0•0•Updated Dec 13, 2019Dec 13, 2019
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