Kits step in the workflow bar

Use the Kits step in the workflow bar to set up information that is needed for sample preparation and sequencing, including the chip and kits used. Options that are available in the Kits step depend on the instrument used. Selections in this step influence how the data are analyzed after sequencing.

  1. In the Kits step in the workflow bar, enter or select the following information.

    Item

    Selection

    Instrument

    Select the sequencing instrument system being used, for example, Ion PGM™ System.

    Sample Preparation Kit

    (Optional) Select the sample preparation kit used.

    Library Kit Type

    Select the kit used to prepare the library (for example, Ion AmpliSeq™ Library Kit Plus).

    Template Kit

    1. Select the instrument system used: OneTouch, IonChef, or IA.

    2. Select the templating kit used.

    Sequencing Kit

    Select the sequencing kit used (for example, Ion S5™ Sequencing Kit).

    Chip Type

    Select the sequencing chip type to be used (for example, Ion 540™ Chip).

    Control Sequence

    (Optional) Select the control sequence added to the library preparation. Leave blank if not used.

    Barcode Set

    Select the barcode set used (for example, IonXpress).

    Flows

    Enter the number of nucleotide reagent flows required to complete the sequencing run (for example, 400).

    Mark as Duplicate Reads

    Select this option to mark duplicate reads in the BAM file after a run is completed. Do not use with Ion AmpliSeq™ data.

    For more information, see About the Mark as Duplicates Reads option.

    To remove marked duplicates from the BAM file, select the FilterDuplicates plugin in the Plugins step in the workflow bar.

    For more information, see Plugins step in the workflow bar.

    Enable Realignment

    Select this option to perform realignment, an optional step that is executed immediately after TMAP. This step adjusts the alignment, primarily in the CIGAR string.

    For more information, see TMAP modules.

  2. (Optional) In Advanced Settings, click Customize to customize the Advanced Settings parameters.

    For more information, see Advanced Settings—Kits step in workflow bar.

    IMPORTANT! We recommend using the default settings. Consult your local Field Service Engineer before modifying advanced settings.

    Setting

    Description

    Templating Protocol

    Script that the Ion Chef™ Instrument follows to perform the templating reaction. We recommend that you do NOT change this setting.

    Forward Library Key

    Select your forward library key, if you have one.

    Test Fragment Key

    Enter your test fragment key.

    Base Calibration Mode

    Select one of the following base calibration options:

    • Default Calibration—allows a random subset of wells to be used for base calibration. This option uses TMAP to align the training subset of wells and is recommended if a good reference for the template is available.

    • Enable Calibration Standard—allows wells belonging to the Calibration Standard to be selected as the training subset.

    • Blind Calibration—uses the same random subset of wells as Default Calibration but does not require an alignment step to generate the calibration model. This option is recommended if the template does not align well to a reference genome or if no reference is specified.

    • No Calibration

    See your template kit user guide for more details.

    Forward 3' Adapter

    Select your forward 3' adapter.

    Flow Order

    Select the flow order. For more information, see flow order.

  3. Click Next in the workflow bar to continue with the Planned Run or with Planned Run template creation.
Related Topics
Parent topic: Steps in the workflow bar
Child Topics
Advanced Settings—Kits step in workflow bar
About the Mark as Duplicates Reads option