Pinned Repositories
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
DEGEPRIME
A program for degenerate primer design for broad taxonomic-range PCR for microbial ecology studies
LabProtocols
The Environmental Genomic Group also does lab work. This is how we do it.
metagenomics-workshop
Metagenomics Workshop
mix_assembly_pipeline
Mix_assembly gene catalog pipeline
POGENOM
Population genomics from metagenomes
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.
Environmental Genomics Group SciLifeLab/KTH Stockholm's Repositories
EnvGen/DEGEPRIME
A program for degenerate primer design for broad taxonomic-range PCR for microbial ecology studies
EnvGen/metagenomics-workshop
Metagenomics Workshop
EnvGen/snakemake-workflows
Common Snakemake rules and workflows mainly directed towards Metagenomic analysis.
EnvGen/toolbox
Various scripts used at the EnvGen group, directed towards metagenomic analysis.
EnvGen/LabProtocols
The Environmental Genomic Group also does lab work. This is how we do it.
EnvGen/POGENOM
Population genomics from metagenomes
EnvGen/BARM_tools
A set of tools that are useful to reuse the Baltic Sea Reference Metagenome
EnvGen/BLUEPRINT_pipeline
The bioinformatics pipeline used in the BLUEPRINT project
EnvGen/mix_assembly_pipeline
Mix_assembly gene catalog pipeline
EnvGen/Tutorials
A few guides in how to use our tools, and some other people's tools as well.
EnvGen/2015-10-sediment
Metagenomics on sea floor sediment.
EnvGen/BARM_web_server
Baltic sea Reference Metagenome web server
EnvGen/euk_popgen
collaborative scripting forn the euk_popgen project
EnvGen/2015-05-Moose-Microbiome
Tracking of annotation and analysis of Moose Microbiome
EnvGen/2015-10_capnocytophaga_prokka_extended
EnvGen/B1-Ocean
EnvGen/BARM_workdir
A repository to keep track of the generation and preliminary analysis of the BAltic sea Refernce Metagenome
EnvGen/BLUEPRINT_reference_binning_dir
This repo is used for running the blueprint pipeline.
EnvGen/CompProtocols
Computational Protocols
EnvGen/cookiecutter-binning-project
A template repository for starting a new binning project using the snakemake-workflows.
EnvGen/cookiecutter-binning-project-demo
A demo for the cookiecutter-binning-project repository.
EnvGen/Degprimer_design
EnvGen/Degprimer_specificity
EnvGen/EMBLmyGFF3
An efficient way to convert gff3 annotation files into EMBL format ready to submit.
EnvGen/envgen.github.io
The Environmental Genomics Home Page
EnvGen/Gene_Catalog_Rshiny
Rshiny app - Gene catalog using mix-assembly approach
EnvGen/moose_data_analysis
EnvGen/phyloBOTL
Phylogeny-based Ortholog-trait Linkage pipeline
EnvGen/preprocessing
A directory to keep snakemake rules for preprocessing metagenomic reads
EnvGen/prokka
Rapid prokaryotic genome annotation