Hisat2 with many files

Question

[Molinia]

Hello!

Okay so here is my question I have multiple samples that I want to align (R1 and R2 for 8 different samples.. So I know basically how hisat2 works Hisat2 -x indexed genome -f1 -f2 -s output.sam But i dont want to do it for each file.. I have seen that to perform this we can do a loop on those files, but I wanted to know how you do it with a parallel? I've also checked the gnu documentation but not sure i've understand

Thanks in advance

[ATpoint]

What have you tried? Here is some inspiration towards GNU parallel. Keep in mind that extensive parallelization only makes sense if you have the CPU and memory resources on a powerful workstation or cluster. If you have only moderate resources (say like < 16 CPUs and single or low-double digit RAM) better use a loop as parallelization will probably not give any gains in speed. A: Optimize bwa mem in parallel on a SLURM cluster

[Molinia]

Ok thanks I"ll check this out !!