Hi, I have several .fastq (R1 and R2) files in a directory. For example files: 9-Lmm05-P1413070_S9_L001_R1_001.fastq.gz, 9-Lm05-P1413070_S9_L001_R2_001.fastq.gz. I want to run the following command for the all fastq files in the directory and generate separate output directories for each pair (R1 and R2) by their prefix name (e.g. 9-Lmm05-P1413070).
$spades.py -k 21,33,55,77 -1 file1_R1_001.fastq.gz -2 file2_R2_001.fastq.gz -o Assembly
Could you please help to suggest a perl/python script to perform that.