Library Key

Enter the sequence used to identify library reads. Example: "TCAG".

TF key

Enter the sequence used to identify test fragment reads. Example: "ATCG".

3' Adapter

Enter the name and sequence of the 3' adapter.

Mark as Duplicate Reads

Enable Filter out PCR duplicates. Useful when reanalyzing combined BAM files. Do not use with Ion AmpliSeq™ data.

Base Calibration Mode

Select one of the four options that are available: Default Calibration, Enable Calibration Standard, Blind Calibration, and No Calibration.

Enable Realignment

(Optional) Perform realignment, an optional analysis step that is executed right after TMAP. This step adjusts the alignment, primarily in the CIGAR string.