Environmental Genomics Group SciLifeLab/KTH Stockholm

Login: EnvGen

Company: null

Location: KTH / Science for Life Laboratory

email: anders.andersson@scilifelab.se

Blog: http://envgen.github.io/

Members

  1. Anders Andersson
  2. Ino de Bruijn
  3. Johannes Alneberg

Repositories

2015-05-Moose-Microbiome
Tracking of annotation and analysis of Moose Microbiome
2015-10_capnocytophaga_prokka_extended
null
2015-10-sediment
Metagenomics on sea floor sediment.
BARM_tools
A set of tools that are useful to reuse the Baltic Sea Reference Metagenome
BARM_web_server
Baltic sea Reference Metagenome web server
BARM_workdir
A repository to keep track of the generation and preliminary analysis of the BAltic sea Refernce Metagenome
Binning
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
BLUEPRINT_pipeline
The bioinformatics pipeline used in the BLUEPRINT project
BLUEPRINT_reference_binning_dir
This repo is used for running the blueprint pipeline.
CompProtocols
Computational Protocols
cookiecutter-binning-project
A template repository for starting a new binning project using the snakemake-workflows.
cookiecutter-binning-project-demo
A demo for the cookiecutter-binning-project repository.
DEGEPRIME
A program for degenerate primer design for broad taxonomic-range PCR for microbial ecology studies
EMBLmyGFF3
An efficient way to convert gff3 annotation files into EMBL format ready to submit.
envgen.github.io
The Environmental Genomics Home Page
LabProtocols
The Environmental Genomic Group also does lab work. This is how we do it.
metagenomics-workshop
Metagenomics Workshop
moose_data_analysis
null
POGENOM
Population genomics from metagenomes
preprocessing
A directory to keep snakemake rules for preprocessing metagenomic reads
prokka
Rapid prokaryotic genome annotation
snakemake-workflows
Common Snakemake rules and workflows mainly directed towards Metagenomic analysis.
toolbox
Various scripts used at the EnvGen group, directed towards metagenomic analysis.
Tutorials
A few guides in how to use our tools, and some other people's tools as well.
This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.