- folder which contains reference database files. You can built a reference database by following the instructions [here](projet_builtdatabase).
- folder which contains pairend-end raw reads `.fastq.gz` files and the sample description `.dat` files. Raw reads files from the same pair must be named as `*_R1.fastq.gz` and `*_R2.fastq.gz` where wildcard `*` is the name of the sequencing run. The alphanumeric order of the names of sample description `.dat` files must be the same than the names of paired-end raw reads `.fastq.gz` files. The sample description file is a text file where each line describes one sample. Columns are separated by space or tab characters. Sample description file is described [here](https://pythonhosted.org/OBITools/scripts/ngsfilter.html).
order of arguments is important : 1) path to the folder which contains paired-end raw reads files and sample description file 2) path to the folder which contains reference database files 3) number of available cores (here for instance 16 cores)