MinION + MinIT generated long reads data analysis pipeline for detection and classification of genomic sample(s) {MINDS}
You will need to download miniconda as described in the link below;
https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html
Setup an conda environment using miniconda
-
conda env create --file requirements.yml
-
source activate MINDS
-
mkdir projects
-
cd projects
-
mkdir MINDS
create the following folders inside the MINDS folder.
a. centrifuge_db
b. centrifuge_rslts
c. code
d. docs
e. fastq
f. logs
g. reports
- Download the centrifuge specific database indexes from https://ccb.jhu.edu/software/centrifuge/
- Move or copy the database index files into the centrifuge_db folder
source activate MINDS
source deactivate
source activate MINDS
cd projects/MINDS/code
jupyter notebook
Click on MINDS.ipynb to open the notebook and execute the pipeline.
Reports generated by the pipeline are stored in the /MINDS/centrifuge_rslts folder.