The test data used for this workflow was provided by the authors of 'Developing standards for the microbiome field' (publication available here) The data from the study (NCBI Bioproject ID PRJNA622674) can be accessed here
- Clone the github repo at and navigate to the directory
git clone https://github.com/MGordon09/metagenomics_mpa3.git \ cd metagenomics_mpa3
- Create a conda enviroment to perform the analysis by running the following (NB environment must be named metaphlan3)
conda env create --name metaphlan3 --file=environment_test.yml
-
For linux users, edit the bowtie2 installation section of
prepare_metaphlandb.sh
script in theprepare_metaphlan()
process (section commented in code). Linux users will also need to modifyrun_metaphlan3.sh
script in therun_metaphlan()
process (also highlighted in code) (Other bowtie2 releases available here -
Run the
prepare_metaphlandb.sh
script. This will take some time to run as it downloads and constructs the metaphlan reference database.
./prepare_metaphlandb.sh
-
Change the
$READS
and$LINKPATH_DB
file paths in therun_metagenomics.sh
script. The$READS
path should point to the folder containing your reads. The$LINKPATH_DB
will point to the folder storing the metaphlan reference database (given as output byprepare_metaphlandb.sh
)READS=/FULL/PATH/TO/data/ LINKPATH_DB=/FULL/PATH/TO/reference
-
Finally, run the
run_metagenomics.sh
script. (Dont forget toprepare_metaphlandb.sh
if running on linux! )./run_metagenomics.sh