This mode trims reads to remove adapter sequences. It is implemented by edu.cornell.med.icb.goby.modes.TrimMode.java.
The following options are available in this mode
|input||yes||Name of the compact input file.|
|output||yes||Name of the fasta file output.|
|adapters||yes||Name of the file with the sequence of the adapters (one sequence per line)|
|n/a||no||When this switch is provided, the complement of the adapter sequences are also trimmed. Default value: FALSE|
|min-left-length||no||Minimum number of bases the adapter must match on the left to be trimmed. Default value: 0|
|min-right-length||no||Minimum number of bases the adapter must match on the right to be trimmed. Default value: 0|