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The cutadapt command line call provides the -j CORES, --cores CORES option to allow you to run over multiple cores. Call cutadapt --help for more information.
Using cutadpat with dada2
We have had a number of researchers using cutadapt within dada2 related R scripts, as detailed under DADA2 ITS Pipeline Workflow (1.8). Following this page, below is one example of how to use cutadapt, within your dada2 related script.
Step 1 Load Module
Within your bash script you will need to first load the cutadapt module:
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... module load cutadapt/2.10 ... srun Rscript dada2_code.R ... |
Behind the scenes, this will add the path to the cutadapt binary into your environment variables.
Step 2 Make System Call in R Code
The next step is to make a system call from within your R script that calls cutadapt.
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