Hisat2 with many files

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4.5 years ago

Molinia ▴ 10

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

alignment hisat • 1.1k views

ADD COMMENT • link 4.5 years ago by Molinia ▴ 10

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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