@EnvGen

Environmental Genomics Group SciLifeLab/KTH Stockholm

  • Various scripts used at the EnvGen group, directed towards metagenomic analysis.

    Python 1 MIT Updated Jun 30, 2018
  • Common Snakemake rules and workflows mainly directed towards Metagenomic analysis.

    Python 10 6 MIT Updated Jun 21, 2018
  • Baltic sea Reference Metagenome web server

    Python GPL-2.0 Updated Mar 19, 2018
  • Population genomics from metagenomes

    Perl BSD-2-Clause Updated Jan 15, 2018
  • A directory to keep snakemake rules for preprocessing metagenomic reads

    Python Updated Jan 12, 2018
  • An efficient way to convert gff3 annotation files into EMBL format ready to submit.

    Python 5 GPL-3.0 Updated Nov 22, 2017
  • A set of tools that are useful to reuse the Baltic Sea Reference Metagenome

    Python 1 Updated Oct 18, 2017
  • A program for degenerate primer design for broad taxonomic-range PCR for microbial ecology studies

    Perl 2 6 Updated Jun 9, 2017
  • The Environmental Genomic Group also does lab work. This is how we do it.

    10 5 Updated Jun 7, 2017
  • A template repository for starting a new binning project using the snakemake-workflows.

    Python Updated Apr 19, 2017
  • Metagenomics on sea floor sediment.

    Python Updated Apr 10, 2017
  • The bioinformatics pipeline used in the BLUEPRINT project

    Python 1 Updated Jan 25, 2017
  • A repository to keep track of the generation and preliminary analysis of the BAltic sea Refernce Metagenome

    Updated Jan 5, 2017
  • Metagenomics Workshop

    Python 7 29 Updated Nov 23, 2016
  • A few guides in how to use our tools, and some other people's tools as well.

    Perl 3 Updated Nov 17, 2016
  • The Environmental Genomics Home Page

    HTML 2 Updated Oct 20, 2016
  • Jupyter Notebook 1 Updated Mar 10, 2016
  • Python Updated Oct 19, 2015
  • This repo is used for running the blueprint pipeline.

    Updated Oct 19, 2015
  • Tracking of annotation and analysis of Moose Microbiome

    Python 1 Updated Sep 23, 2015
  • A demo for the cookiecutter-binning-project repository.

    Shell MIT Updated May 7, 2015
  • Rapid prokaryotic genome annotation

    Perl 84 Updated Apr 29, 2015
  • Computational Protocols

    MIT Updated Sep 24, 2014
  • Scripts required to calculate tetramer frequencies and create input files for ESOM. See: Dick, G.J., A. Andersson, B.J. Baker, S.S. Simmons, B.C. Thomas, A.P. Yelton, and J.F. Banfield (2009). Community-wide analysis of microbial genome sequence signatures. Genome Biology, 10: R85

    Perl 10 Updated Nov 27, 2013