It would be great if cutadapt could accept multiple FastQ files (or FastQ pairs, for paired data) as input, and write the trimmed reads to the same output file(s). This would allow users to merge and trim their FastQ data in a single step, thus saving the time for reading and writing all data to disk twice (once for merging, and once for cutadapt).
This behaviour is already possible with a helper script, as is shown here, but it would be nice if Cutadapt could support this out of the box.
It would be great if cutadapt could accept multiple FastQ files (or FastQ pairs, for paired data) as input, and write the trimmed reads to the same output file(s). This would allow users to merge and trim their FastQ data in a single step, thus saving the time for reading and writing all data to disk twice (once for merging, and once for cutadapt).
This behaviour is already possible with a helper script, as is shown here, but it would be nice if Cutadapt could support this out of the box.