Questions & Answers

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  • How do I know if the MiSeq FGx run met the specifications?

    The run has met the Illumina specifications when the run metrics are within the thresholds and are colored green.

  • Can the MiSeq FGx be used for RUO applications?

    Yes. The MiSeq FGx Control Software offers an RUO run option alongside the Forensic Genomics run options. The RUO side of the software is fully compatible with all Illumina-supported RUO run types, and runs are set up as for standard MiSeq runs. For more details on set-up and workflow, see the MiSeq FGx Instrument Reference Guide.


  • How is it possible to combine multiple samples into one MiSeq FGx sequencing run?

    Multiple samples can be pooled together because of the use of unique index (barcode) sequences added during library preparation. Indexes allow the software to separate out the data for each individual sample after sequencing.

  • How long can ForenSeq DNA Signature Prep libraries be stored before being sequenced?

    Final pooled libraries can be stored at -25°C to -15°C for up to 3 months.


  • How long does it take to prepare and sequence libraries from my samples using the MiSeq FGx Forensic Genomics System?

    Preparing libraries takes approximately 9 hours. Sequencing and Real-Time Analysis (RTA) software tasks on the MiSeq FGx such as image processing, assigning base calls, and then designating a quality score for each base call takes approximately 30 hours. Aligning reads to provide sample information, along with optional steps such as generating reports, population statistics, sample comparison, phenotype estimations and bio-geographical ancestry estimations take approximately 1 hour.

  • Can a MiSeq FGx run be started when the server is switched off?

    To log in to MiSeq FGx Control Software, a connection must be established with the ForenSeq Universal Analysis Software server to check authentication. After authentication, an RUO run can be performed without connection to the server. There is a buffering mechanism with the MiSeq FGx Control Software to allow data transmission to resume upon a connection loss to ForenSeq Universal Analsyis Software during acquisition.

  • Can the sample sheet for the MiSeq FGx run be created using the Illumina Experiment Manager (IEM)?

    No. However, a sample sheet created using IEM is compatible with the RUO mode of the MiSeq FGx Control Software. For forensic runs, the samples are defined in the ForenSeq Universal Analysis Software before acquisition through a file upload or manual entry. For details on the information in the file, see the ForenSeq Universal Analsyis Software Guide.

  • What if I do not have an account for the ForenSeq Universal Analysis Software when the MiSeq FGx Control Software asks for login details?

    An account can be set up on the ForenSeq Universal Analysis Software. See the ForenSeq Universal Analysis Software Guide for more details. This account is used on the sequencing instrument to log in to MiSeq FGx Control Software and start the runs created by the account holder on the ForenSeq Universal Analysis Software.

  • How long do the different washes on the MiSeq FGx take?

    The post-run wash takes 30 minutes and a maintenance wash takes about 1 hour.

  • Do I have to wash the MiSeq FGx between sequencing runs?

    Yes, the MiSeq FGx needs must be washed between runs to remove any remaining reagents from the fluidics lines and make sure that they are clean before the next run is started. The MiSeq FGx offers a bleach post-run wash protocol that minimizes run-to-run contamination.  See the MiSeq FGx Instrument Reference Guide for wash instructions.


  • Can the MiSeq FGx run monitoring data be viewed after the run has completed?

    Yes, the same metrics that are shown during data acquisition are available on the ForenSeq Universal Analysis Software after the run is complete.

  • Do I have to have the server with ForenSeq Universal Analysis Software connected to the MiSeq FGx?

    Yes, in order for the results to be transferred from the MiSeq FGx to the ForenSeq Universal Analysis Software a connection must exist between the systems. In many cases that connection is established through the company network. However, in some labs that connection can be on a local network created with the provided router.


  • How do I analyze MiSeq FGx data?

    Data analysis is performed using the ForenSeq Universal Analysis Software.

  • Can I evaluate data from multiple MiSeq FGx runs to compare in the analysis software?

    Yes. Direct sample to sample comparison can be performed using the ForenSeq Universal Analysis software.