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--min-length

Reads with length below N bp after demultiplexing are omitted. The default is 50. ZMWs with no reads passing are omitted.

--max-input-length

Reads with length above N bp are omitted for scoring in the demultiplexing step. The default is 0, meaning deactivated.

--min-score

Threshold for the average barcode score of the leading and trailing ends. ZMWs with barcode score below N are omitted. The default is 0. It is advised to set it to 26 for CLR and 80 for HiFi.

--min-passes

ZMWs with less than N full passes, a read with a leading and trailing adapter, are omitted. This is only useful for CLR data. CCS / HiFi data ignore this option. The default is 0, no full-pass needed. Example

0 pass  : insert - adapter - insert
1 pass  : insert - adapter - INSERT - adapter - insert
2 passes: insert - adapter - INSERT - adapter - INSERT - adapter - insert

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