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    31 repositories

    • zAMP

      Public
      zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics
      snakemakepipelinemetagenomicsamplicon
      R
      •
      MIT License
      •5•8•8•0•Updated Feb 6, 2025Feb 6, 2025

    • diag_pipelines

      Public
      Pipelines dealing with high throughput sequencing data for microbiology diagnostic procedures. Documentation available at http://metagenlabdiag-pipelines.readthedocs.io/en/latest/ and Docker images at https://hub.docker.com/r/metagenlab/diag_pipelines/.
      bioinformaticssnakemakegenomicsmicrobiologyconda-environment
      Python
      •9•7•5•1•Updated Jan 28, 2025Jan 28, 2025

    • zDB

      Public
      zDB: comparative bacterial genomics made easy
      HTML
      •
      MIT License
      •4•32•2•1•Updated Jan 22, 2025Jan 22, 2025

    • MeSS

      Public
      Snakemake pipeline for simulating shotgun metagenomic samples
      bioinformaticssnakemake-workflowshotgun-metagenomics
      Python
      •
      MIT License
      •2•22•3•0•Updated Jan 21, 2025Jan 21, 2025

    • assembly_finder

      Public
      snakemake-powered cli to download genomes using NCBI datasets
      Python
      •
      MIT License
      •0•13•0•0•Updated Jan 20, 2025Jan 20, 2025

    • zAMPExplorer

      Public
      zAMPExplorer: Shiny app for amplicon data visualization and stats
      R
      •2•0•0•1•Updated Jan 16, 2025Jan 16, 2025

    • metagenlab.r-universe.dev

      Public
      0•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.3k•0•0•0•Updated Jan 9, 2025Jan 9, 2025

    • EpiPlot

      Public
      R
      •1•0•0•0•Updated Jan 9, 2025Jan 9, 2025

    • PIPOVAP

      Public
      Lung and gut microbiota profiling in intensive care unit patients: a prospective pilot study
      MIT License
      •0•0•0•0•Updated Jan 1, 2025Jan 1, 2025

    • benchmark-MeSS-CAMISIM

      Public
      Nextflow pipeline to benchmark MeSS and CAMISIM
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Dec 16, 2024Dec 16, 2024

    • MeSS-figures

      Public
      Supplementary figures and scripts for the MeSS paper
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 16, 2024Dec 16, 2024

    • configs

      Public
      Config files used to define parameters specific to compute environments at different Institutions
      Nextflow
      •
      MIT License
      •285•0•0•0•Updated Nov 29, 2024Nov 29, 2024

    • MASRES

      Public
      Nextflow
      •0•2•0•0•Updated Oct 28, 2024Oct 28, 2024

    • phanta

      Public
      Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
      Python
      •
      MIT License
      •9•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • GENCOV

      Public
      Python
      •
      GNU General Public License v3.0
      •0•5•1•0•Updated Oct 14, 2024Oct 14, 2024

    • locus2genoplotr

      Public
      Plot bacterial gene maps and genome comparison plots from command line with genoPlotR and GenomeDiagram
      Python
      •1•10•1•0•Updated Aug 20, 2024Aug 20, 2024

    • chlamdb

      Public
      chlamdb.ch website code
      HTML
      •1•5•4•0•Updated Aug 20, 2024Aug 20, 2024

    • metagenlab_libs

      Public
      Python
      •0•0•0•1•Updated Apr 30, 2024Apr 30, 2024

    • rnaseq

      Public
      Rnaseq pipeline
      Python
      •0•0•0•0•Updated Feb 1, 2024Feb 1, 2024

    • mummer2circos

      Public
      Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments
      Python
      •
      MIT License
      •24•101•7•0•Updated Dec 11, 2023Dec 11, 2023

    • extractmag

      Public
      Extract MAG of a specific taxon of interest from metagenome assembly
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 16, 2023Oct 16, 2023

    • nanopore

      Public
      Nextflow
      •0•2•0•0•Updated Feb 9, 2023Feb 9, 2023

    • BioVx

      Public
      The Extended BioV suite of programs (fully written in Python)
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated May 10, 2022May 10, 2022

    • TPutils

      Public
      Python
      •3•4•0•0•Updated Apr 13, 2022Apr 13, 2022

    • core_genome_phylogeny

      Public
      Build a phylogeny with FastTree based on a concatenated alignment of 103 marker genes identified with checkM.
      Python
      •0•0•0•0•Updated Oct 22, 2021Oct 22, 2021

    • microbiome_shotgun_pipeline

      Public
      Snakemake pipeline for shotgun metagenomics
      Python
      •0•3•0•0•Updated May 5, 2021May 5, 2021

    • MGE_identifier

      Public
      Python
      •0•0•0•0•Updated Jan 14, 2020Jan 14, 2020

    • updated_simulate_PCR

      Public
      Corrected version of simulate_PCR (https://doi.org/10.1186/1471-2105-15-237)
      Perl
      •
      Other
      •1•3•2•0•Updated Aug 2, 2019Aug 2, 2019

    • blast2profile

      Public
      Python
      •0•0•0•0•Updated Jan 17, 2018Jan 17, 2018