Short reads data from history. This could be reads before trimming.

Short reads data from history. This could be reads after trimming.

Specifies a non-default file which contains the list of adapter sequences which will be explicitly searched against the library. The file must contain sets of named adapters in the form name[tab]sequence. Lines prefixed with a hash will be ignored.

Specifies a non-default file which contains a set of criteria which will be used to determine the warn/error limits for the various modules. This file can also be used to selectively remove some modules from the output all together. The format needs to mirror the default limits.txt file found in the Configuration folder.