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    28 repositories

    • MeSS

      Public
      Snakemake pipeline for simulating shotgun metagenomic samples
      bioinformaticssnakemake-workflowshotgun-metagenomics
      Python
      •
      MIT License
      •3•18•5•1•Updated Oct 26, 2024Oct 26, 2024

    • zAMP

      Public
      zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics
      snakemakepipelinemetagenomicsamplicon
      R
      •
      MIT License
      •5•8•7•0•Updated Oct 24, 2024Oct 24, 2024

    • assembly_finder

      Public
      snakemake-powered cli to download genomes using NCBI datasets
      Python
      •
      MIT License
      •0•12•0•0•Updated Oct 24, 2024Oct 24, 2024

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.3k•0•0•0•Updated Oct 24, 2024Oct 24, 2024

    • zAMPExplorer

      Public
      zAMPExplorer
      R
      •1•0•0•1•Updated Oct 24, 2024Oct 24, 2024

    • MeSS-figures

      Public
      Supplemental code for reproducing MeSS paper figures
      Jupyter Notebook
      •0•0•0•0•Updated Oct 23, 2024Oct 23, 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

    • 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•6•5•1•Updated Oct 17, 2024Oct 17, 2024

    • configs

      Public
      Config files used to define parameters specific to compute environments at different Institutions
      Nextflow
      •
      MIT License
      •271•0•0•0•Updated Oct 17, 2024Oct 17, 2024

    • GENCOV

      Public
      Python
      •
      GNU General Public License v3.0
      •0•4•1•0•Updated Oct 14, 2024Oct 14, 2024

    • benchmark-MeSS-CAMISIM

      Public
      Nextflow pipeline to benchmark MeSS and CAMISIM
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Sep 20, 2024Sep 20, 2024

    • zDB

      Public
      zDB: comparative bacterial genomics made easy
      HTML
      •
      MIT License
      •4•29•3•0•Updated Sep 18, 2024Sep 18, 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

    • MASRES

      Public
      Nextflow
      •0•2•0•0•Updated Aug 12, 2024Aug 12, 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•99•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•1•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

    • MultiQC

      Public
      Forking MultiQC in order to add to the parsing of qualimap results the extraction of the "General Error Rate". Will PR back there once performed
      Python
      •
      GNU General Public License v3.0
      •600•0•0•0•Updated Jan 8, 2018Jan 8, 2018