Environmental Genomics Group SciLifeLab/KTH Stockholm's repositories
metagenomics-workshop
Metagenomics Workshop
snakemake-workflows
Common Snakemake rules and workflows mainly directed towards Metagenomic analysis.
LabProtocols
The Environmental Genomic Group also does lab work. This is how we do it.
BARM_tools
A set of tools that are useful to reuse the Baltic Sea Reference Metagenome
BLUEPRINT_pipeline
The bioinformatics pipeline used in the BLUEPRINT project
2015-10-sediment
Metagenomics on sea floor sediment.
BARM_web_server
Baltic sea Reference Metagenome web server
euk_popgen
collaborative scripting forn the euk_popgen project
2015-05-Moose-Microbiome
Tracking of annotation and analysis of Moose Microbiome
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_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.
EMBLmyGFF3
An efficient way to convert gff3 annotation files into EMBL format ready to submit.
envgen.github.io
The Environmental Genomics Home Page
Gene_Catalog_Rshiny
Rshiny app - Gene catalog using mix-assembly approach
mix_assembly_pipeline
Mix_assembly gene catalog pipeline
preprocessing
A directory to keep snakemake rules for preprocessing metagenomic reads