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2015-05-moose-microbiome

Tracking of annotation and analysis of Moose Microbiome

2015-10-sediment

Metagenomics on sea floor sediment.

2015-10_capnocytophaga_prokka_extended

b1-ocean

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

degprimer_design

degprimer_specificity

emblmygff3

An efficient way to convert gff3 annotation files into EMBL format ready to submit.

envgen.github.io

The Environmental Genomics Home Page

euk_popgen

collaborative scripting forn the euk_popgen project

gene_catalog_rshiny

Rshiny app - Gene catalog using mix-assembly approach

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

moose_data_analysis

phylobotl

Phylogeny-based Ortholog-trait Linkage pipeline

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.