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Various scripts used at the EnvGen group, directed towards metagenomic analysis.
Common Snakemake rules and workflows mainly directed towards Metagenomic analysis.
Baltic sea Reference Metagenome web server
Population genomics from metagenomes
A directory to keep snakemake rules for preprocessing metagenomic reads
An efficient way to convert gff3 annotation files into EMBL format ready to submit.
A set of tools that are useful to reuse the Baltic Sea Reference Metagenome
A program for degenerate primer design for broad taxonomic-range PCR for microbial ecology studies
The Environmental Genomic Group also does lab work. This is how we do it.
A template repository for starting a new binning project using the snakemake-workflows.
Metagenomics on sea floor sediment.
The bioinformatics pipeline used in the BLUEPRINT project
A repository to keep track of the generation and preliminary analysis of the BAltic sea Refernce Metagenome
A few guides in how to use our tools, and some other people's tools as well.
The Environmental Genomics Home Page
This repo is used for running the blueprint pipeline.
Tracking of annotation and analysis of Moose Microbiome
A demo for the cookiecutter-binning-project repository.
Rapid prokaryotic genome annotation
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