Input Checks

Items to check before submitting your analysis

Input Validation Steps

In addition to sample sheet validation, before starting an analysis, the software performs the following checks:

• Resource bundle integrity

• DRAGEN license validity

• NEW in v2.6.2! Instrument Type determination

Instrument type is required by the software because different instrument platforms produce output with distinct systematic noise profiles. DRAGEN TSO 500 analysis software requires instrument-specific baseline noise files. Before kicking off analysis, the software determines the instrument type in order to select which baseline files to use. This means that even when starting from FASTQ, all samples in the run must be sequenced on the same type of instrument.

Instrument Type Determination for Baselines

When starting analysis from BCL files, the software references the RunInfo.xml file in the Run folder to identify the sequencing instrument type. For analyses beginning with FASTQ files, the software reads the FASTQ file headers for this information. Correct baselines for variant calling are then applied based on the determined instrument type.

For analysis starting from FASTQ files, if a mixed instrument type is detected, the software will exit with an error.

The Combined Variant Output File will include the instrument type Combined Variant Output

Baselines are selected based on a combination of Library Prep Kit and Instrument Type.

• Library Prep Kit: TSO500_v2

  • Instrument Types:

    • NovaSeq 6000, NovaSeq 6000Dx, NextSeq 500, NextSeq 550: Use one set of baselines.

    • NextSeq 1000/ 2000: Use a different set of baselines.

    • NovaSeqX, NovaSeqXPlus: Use another set of baselines.

• Library Prep Kit: TSO500 or TSO500HT

  • A single set of baselines applies to all instrument types.

If instrument type is undetermined (ie not matching any of the below), the software will set instrument type to NA, and the baselines for NovaSeq 6000, NovaSeq 6000Dx, NextSeq 500, and NextSeq 550 will be applied.

/Run/Instrument in RunInfo.xml or Header of the FASTQ GZ Files Starts With	Instrument Type
A	NovaSeq6000
ADX	NovaSeq6000Dx
NS50 or NB50 or NL50	NextSeq500
NS55 or NB55 or NDX	NextSeq550
VH	NextSeq1k2k
LH	NovaSeqXPlus
LL	NovaSeqX