Repositories list

• Degprimer_design

  Public
  Python

  •1•0•0•0•Updated Oct 9, 2024Oct 9, 2024

• POGENOM

  Public
  Population genomics from metagenomes

  Perl

  •

  BSD 2-Clause "Simplified" License

  •4•11•7•0•Updated Sep 1, 2024Sep 1, 2024

• phyloBOTL

  Public
  Phylogeny-based Ortholog-trait Linkage pipeline

  Python

  •0•0•0•0•Updated Apr 14, 2024Apr 14, 2024

• mix_assembly_pipeline

  Public
  Mix_assembly gene catalog pipeline

  Python

  •0•1•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

• envgen.github.io

  Public
  The Environmental Genomics Home Page

  HTML

  •2•0•0•0•Updated Feb 12, 2024Feb 12, 2024

• Degprimer_specificity

  Public
  Python

  •1•0•0•0•Updated Dec 20, 2023Dec 20, 2023

• DEGEPRIME

  Public
  A program for degenerate primer design for broad taxonomic-range PCR for microbial ecology studies

  Perl

  •

  Other

  •11•29•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•28•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

  •226•0•0•0•Updated Apr 29, 2015Apr 29, 2015

• CompProtocols

  Public
  Computational Protocols

  MIT License

  •0•0•0•0•Updated Sep 24, 2014Sep 24, 2014