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@EnvGen Environmental Genomics Group SciLifeLab/KTH Stockholm

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    32 repositories

    • envgen.github.io

      Public
      The Environmental Genomics Home Page
      HTML
      •2•0•0•0•Updated Jan 8, 2026Jan 8, 2026

    • EnvPredict

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

    • Degprimer_specificity

      Public
      Python
      •1•0•0•0•Updated Dec 10, 2025Dec 10, 2025

    • phyloBOTL

      Public
      Phylogeny-based Ortholog-trait Linkage pipeline
      Python
      •0•0•0•0•Updated Sep 23, 2025Sep 23, 2025

    • Degprimer_design

      Public
      Python
      •1•0•0•0•Updated Mar 21, 2025Mar 21, 2025

    • POGENOM

      Public
      Population genomics from metagenomes
      Perl
      •
      BSD 2-Clause "Simplified" License
      •5•12•9•0•Updated Sep 1, 2024Sep 1, 2024

    • mix_assembly_pipeline

      Public
      Mix_assembly gene catalog pipeline
      Python
      •0•2•0•0•Updated Apr 5, 2024Apr 5, 2024

    • Gene_Catalog_Rshiny

      Public
      Rshiny app - Gene catalog using mix-assembly approach
      HTML
      •2•0•0•0•Updated Mar 28, 2024Mar 28, 2024

    • B1-Ocean

      Public
      Python
      •
      MIT License
      •0•0•0•1•Updated Mar 4, 2024Mar 4, 2024

    • DEGEPRIME

      Public
      A program for degenerate primer design for broad taxonomic-range PCR for microbial ecology studies
      Perl
      •
      Other
      •12•32•0•0•Updated Jun 9, 2023Jun 9, 2023

    • euk_popgen

      Public
      collaborative scripting forn the euk_popgen project
      R
      •1•0•0•0•Updated Nov 9, 2022Nov 9, 2022

    • BARM_web_server

      Public
      Baltic sea Reference Metagenome web server
      Python
      •
      GNU General Public License v2.0
      •2•0•11•0•Updated Sep 17, 2021Sep 17, 2021

    • toolbox

      Public
      Various scripts used at the EnvGen group, directed towards metagenomic analysis.
      Python
      •
      MIT License
      •2•14•1•0•Updated Apr 28, 2020Apr 28, 2020

    • LabProtocols

      Public
      The Environmental Genomic Group also does lab work. This is how we do it.
      6•12•0•0•Updated Jul 4, 2019Jul 4, 2019

    • Tutorials

      Public
      A few guides in how to use our tools, and some other people's tools as well.
      Perl
      •2•1•1•0•Updated May 6, 2019May 6, 2019

    • moose_data_analysis

      Public
      Jupyter Notebook
      •2•0•0•0•Updated Dec 10, 2018Dec 10, 2018

    • cookiecutter-binning-project

      Public
      A template repository for starting a new binning project using the snakemake-workflows.
      Python
      •0•0•0•0•Updated Dec 10, 2018Dec 10, 2018

    • BLUEPRINT_pipeline

      Public
      The bioinformatics pipeline used in the BLUEPRINT project
      Python
      •0•1•1•0•Updated Dec 10, 2018Dec 10, 2018

    • snakemake-workflows

      Public
      Common Snakemake rules and workflows mainly directed towards Metagenomic analysis.
      Python
      •
      MIT License
      •6•21•0•0•Updated Nov 15, 2018Nov 15, 2018

    • preprocessing

      Public
      A directory to keep snakemake rules for preprocessing metagenomic reads
      Python
      •0•0•0•0•Updated Jan 12, 2018Jan 12, 2018

    • EMBLmyGFF3

      Public
      An efficient way to convert gff3 annotation files into EMBL format ready to submit.
      Python
      •
      GNU General Public License v3.0
      •15•0•0•0•Updated Nov 22, 2017Nov 22, 2017

    • BARM_tools

      Public
      A set of tools that are useful to reuse the Baltic Sea Reference Metagenome
      Python
      •0•2•0•0•Updated Oct 18, 2017Oct 18, 2017

    • 2015-10-sediment

      Public
      Metagenomics on sea floor sediment.
      Python
      •0•0•0•0•Updated Apr 10, 2017Apr 10, 2017

    • BARM_workdir

      Public
      A repository to keep track of the generation and preliminary analysis of the BAltic sea Refernce Metagenome
      0•0•0•0•Updated Jan 5, 2017Jan 5, 2017

    • metagenomics-workshop

      Public
      Metagenomics Workshop
      Python
      •55•27•13•0•Updated Nov 23, 2016Nov 23, 2016

    • 2015-10_capnocytophaga_prokka_extended

      Public
      Python
      •0•0•1•0•Updated Oct 19, 2015Oct 19, 2015

    • BLUEPRINT_reference_binning_dir

      Public
      This repo is used for running the blueprint pipeline.
      0•0•0•0•Updated Oct 19, 2015Oct 19, 2015

    • 2015-05-Moose-Microbiome

      Public
      Tracking of annotation and analysis of Moose Microbiome
      Python
      •1•0•0•0•Updated Sep 23, 2015Sep 23, 2015

    • cookiecutter-binning-project-demo

      Public
      A demo for the cookiecutter-binning-project repository.
      Shell
      •
      MIT License
      •0•0•0•0•Updated May 7, 2015May 7, 2015

    • prokka

      Public
      Rapid prokaryotic genome annotation
      Perl
      •236•0•0•0•Updated Apr 29, 2015Apr 29, 2015