Commit dfcbfbfa authored by peguerin's avatar peguerin
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Update README.md

parent 07002d99
......@@ -54,7 +54,7 @@ Quickstart
- 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).
4. run the pipeline :
- `bash main.sh /path/to/fastq_dat_files /path/to/reference_database_folder 16`
- order of arguments is important : 1) path to the folder which2) path to the folder which contains paired-end raw reads files and sample description file ; 3) number of cores to assign (here for instance 16 cores)
- order of arguments is important : 1) path to the folder which contains reference database files 2) path to the folder which contains paired-end raw reads files and sample description file 3) number of cores to assign (here for instance 16 cores)
5. run the pipeline step by step :
open the file `main.sh` to see details
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