Closed johnbradley closed 2 years ago
In recent tests the remove_adapters step is the slowest step in the pipeline. This step uses trim_galore: https://github.com/wodanaz/Assembling_viruses/blob/73c9bd5c4dd8318dbbee361423044f9eb564713d/scripts/remove-nextera-adapters.sh#L12 The trim_galore documentation includes a --cores <num> argument:
trim_galore
--cores <num>
-j/--cores INT Number of cores to be used for trimming [default: 1]. ... It seems that --cores 4 could be a sweet spot, anything above has diminishing returns.
Determine if using --cores improves performance.
In recent tests the remove_adapters step is the slowest step in the pipeline. This step uses
trim_galore: https://github.com/wodanaz/Assembling_viruses/blob/73c9bd5c4dd8318dbbee361423044f9eb564713d/scripts/remove-nextera-adapters.sh#L12 The trim_galore documentation includes a--cores <num>argument:Determine if using --cores improves performance.