mgordon09 / metagenomics_mpa3 Goto Github PK

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

1. Clone the github repo at and navigate to the directory

git clone https://github.com/MGordon09/metagenomics_mpa3.git \ cd metagenomics_mpa3

2. 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

3. For linux users, edit the bowtie2 installation section of prepare_metaphlandb.sh script in the prepare_metaphlan() process (section commented in code). Linux users will also need to modify run_metaphlan3.sh script in the run_metaphlan() process (also highlighted in code) (Other bowtie2 releases available here

4. 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

4. Change the $READS and $LINKPATH_DB file paths in the run_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 by prepare_metaphlandb.sh) READS=/FULL/PATH/TO/data/ LINKPATH_DB=/FULL/PATH/TO/reference

5. Finally, run the run_metagenomics.sh script. (Dont forget to prepare_metaphlandb.sh if running on linux! ) ./run_metagenomics.sh