This mode trims reads to remove adapter sequences. It is implemented by edu.cornell.med.icb.goby.modes.TrimMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
(-i|--input)inputyesName of the compact input file.
(-o|--output)outputyesName of the fasta file output.
(-a|--adapters)adaptersyesName of the file with the sequence of the adapters (one sequence per line)
--complementn/anoWhen this switch is provided, the complement of the adapter sequences are also trimmed. Default value: FALSE
--min-left-lengthmin-left-lengthnoMinimum number of bases the adapter must match on the left to be trimmed. Default value: 0
--min-right-lengthmin-right-lengthnoMinimum number of bases the adapter must match on the right to be trimmed. Default value: 0