Environmental metagenomics data analysis

Access the virtual machine:

ssh -p [port] [user]@[ip]
screen -S [sessionname]

Check what your home folder, it is pretty much empty:

pwd
ls -al

We definitely need to configure shared conda environment as described in the useful tips. Activate the environment and check if you can run installed software:

(kau) aln@edu-af-01$ trim_galore 
No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)


Please provide the filename(s) of one or more FastQ file(s) to launch Trim Galore!

USAGE:  'trim_galore [options] <filename(s)>'    or    'trim_galore --help'    for more options

Check data folder, what kind of files it contains?

ls /storage/kau/data/

The data analysis workflow is following: 1. Quality control with fastqc 2. Quality control reports aggregation with multiqc 3. If the quality is not satisfactory — trimming with trim_galore (minimum length of the read is 70, quality threshold — 20) 4. OTU (operational taxonomic unit) calling with MetaPhlan2 5. Summary plots generation with Krona 6. Basic analysis in R with ggplots2

We can start with advanced snakemake example to produce fastqc report, modifying it to contain more rules for our workflow.