I have a large number of samples that I need to assemble using metaspades. They are named as such;
CUH001T1_unclassified_unpaired_R1 and CUH001T1_unclassified_unpaired_R2 CUH002T2_unclassified_unpaired_R1 and CUH002T2_unclassified_unpaired_R2 etc
The script I'm using for this is;
spades.py --meta --pe1-1 CUH002T2_unclassified_paired_R1.fastq --pe1-2 CUH002T2_unclassified_paired_R2.fastq -t 20 -m 400 -o ../metaspades/CUH002T2
Does anyone know how to write a loop for this? I'm sure its relatively easy but I'm very new to bioinformatics and can't figure it out.