This mode is used to decode barcoded reads. See the barcode decoding tutorial for further information. It is implemented by
edu.cornell.med.icb.goby.modes.BarcodeDecoderMode.java. The mode trims barcode and adapters from the input reads, and stores the barcode index in the output files (as an optional barcodeIndex protocol buffer attribute on the Read message).

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
n/ainputyesThe compact alignment file(s) to read as input.
(-o|--output)outputnoThe basename of the output counts.
(-b|--barcode-info)barcode-infonoA tab delimited file with barcode[\t]barcodeIndex\tsampleId
(-x|--max-mismatches)max-mismatchesnoThe maximum number of mismatches allowed in the barcode/adapter to accept the barcode match. Default value: 0
(-l|--minimal-match-length)minimal-match-lengthnoThe minimal match length between read and barcode/adapter to accept the barcode match. Default value: 5
(-e|--extremity)extremitynoThe extremity that contains the barcode. Can be either 3_PRIME or 5_PRIME. Default value: 3_PRIME