is there any option for batch processing?

[foamy1881]

Is there an option to multi process in a loop for all R1 and R2 fastq inside a folder? I have more than 1000 fastqs to process.. Would be tedious to process them one by one.

[jsh58]

Thanks for the question. It is easy to loop through files on the command-line. See this reference for examples of writing loops in bash, and this reference for string (filename) manipulation.