Some advanced parameters could be tweaked using Java properties. This properties could be set in the command line by running the jar file as following:

java -Dreadtools.${property_name}=${property_value} -jar ReadTools.jar ${your_arguments}
Property name Default Description
barcode_index_delimiter - Delimiter between barcode sequence when several indexes are used
barcode_quality_delimiter Delimiter between barcode quality when several indexes are used
max_record_for_quality 1000000 Maximum number of record used to guess the quality of a file
sampling_quality_checking_frequency 1000 Read sampling frequency to check if the quality is really Standard
force_overwrite false Force overwrite of output files (default value)
discarded_output_suffix _discarded Suffix for discarded output file(s)