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
| Flag | Arguments | Required | Description |
|---|---|---|---|
(-i|--input) | input | yes | Name of the compact input file. |
(-o|--output) | output | yes | Name of the fasta file output. |
(-a|--adapters) | adapters | yes | Name of the file with the sequence of the adapters (one sequence per line) |
--complement | n/a | no | When this switch is provided, the complement of the adapter sequences are also trimmed. Default value: FALSE |
--min-left-length | min-left-length | no | Minimum number of bases the adapter must match on the left to be trimmed. Default value: 0 |
--min-right-length | min-right-length | no | Minimum number of bases the adapter must match on the right to be trimmed. Default value: 0 |
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