https://github.com/alberdilab/greenland_mycorrhiza
Bioinformatic respository of the shotgun metagenomic data analyses of the greenlandic mycorrhizal network project
Science Score: 13.0%
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Low similarity (6.3%) to scientific vocabulary
Repository
Bioinformatic respository of the shotgun metagenomic data analyses of the greenlandic mycorrhizal network project
Basic Info
- Host: GitHub
- Owner: alberdilab
- Default Branch: main
- Size: 60.5 KB
Statistics
- Stars: 1
- Watchers: 0
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Greenland mycorrhiza
Bioinformatic respository of the shotgun metagenomic data analyses of the greenlandic mycorrhizal network project
This pipeline must be run in a high computation cluster.
Genome-resolved microbial metagenomics
The pipeline only relies on two software:
- Mamba
- Snakemake
The rest of the many required softwatre are downloaded and installed inside the conda environments.
Prepare working environment
```sh
Load dependencies mamba and snakemake (not needed if they are already installed in root)
module load mamba/1.5.6 snakemake/7.20.0
Create working directory
mkdir greenland_shotgun
Clone metagenomic assembly+binning pipeline repository
cd greenlandshotgun git clone https://github.com/3d-omics/mgassembly.git cd mg_assembly
Create screen session
screen -S greenland_shotgun
Create conda environments and run test data to validate them
It might take 20-30 minutes to download and install all software
./run ```
Prepare the input files
Data files
- Move the raw data files to the 'resources/reads/' directory or create soft links.
```sh
In this example, download reads from ERDA
cd resources/reads/ wget https://sid.erda.dk/shareredirect/dcKtF82NjL/SHIndPCR1AEKDL210009000-1a-AK4939-AK6653HTF5CDSX2L11.fq.gz wget https://sid.erda.dk/shareredirect/dcKtF82NjL/SHIndPCR1AEKDL210009000-1a-AK4939-AK6653HTF5CDSX2L12.fq.gz cd ../../ ```
Owner
- Name: alberdilab
- Login: alberdilab
- Kind: organization
- Repositories: 1
- Profile: https://github.com/alberdilab