QIAseq xHYB Long Reads to Germline Variants (ONT) (beta)
The QIAseq xHYB Long Reads to Germline Variants (ONT) (beta) template workflow identifies phased germline variants from QIAseq xHYB Long Read data and annotates these with exon number and amino acid changes. The workflow also produces a read mapping and a coverage report.
The workflow can be found at:
Template Workflows | LightSpeed Workflows (
) | QIAseq workflows (
) | QIAseq xHYB Long Read (
) | QIAseq xHYB Long Reads to Germline Variants (ONT) (beta) (
)
Options in the following dialogs can be configured:
- Choose where to run If you are connected to a CLC Server via your Workbench, you will be asked where you would like to run the analysis. We recommend that you run the analysis on a CLC Server when possible.
- Specify reference data handling Select the relevant Reference Data Set. QIAseq DNA Pro Panels hg38 will be pre-selected and is recommended for running this workflow. If you have not downloaded the Reference Data Set yet, the dialog will offer the opportunity to download it using the Download to Workbench button. If the QIAseq DNA Pro Panels hg38 reference data set does not contain the needed primers and target regions, a custom reference data set can be created, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Reference_Data_Sets_defining_Custom_Sets.html. Reference data sets for QIAseq Targeted DNA and QIAseq Targeted DNA Ultra panels should not be used with this workflow. The differences in read structure will for example prevent primers from being correctly trimmed. XXXXX Fix after decision on reference sequence.
- LightSpeed Long Reads to Germline Variants
Specify options for the LightSpeed Long Reads to Germline Variants tool:
- Reads (fastq) Press Browse to select fastq files for analysis.
- Masking mode To enable reference masking when mapping reads, set this option and select a masking track.
- Masking track Provide a masking track for the chosen reference genome if reference masking has been enabled.
- Minimum average quality Specify the minimum average quality of detected variants. See Germline variant detection for additional details.
- Minimum allele count Specify the minimum number of reads supporting an identified variant.
- Batch Select if fastq files from different samples are used as input, and each sample should be analyzed individually (for information about batching see Batching).
- Join lanes when batching Select to join fastq files from the same sample that were sequenced on different lanes.
- Target regions Choose the relevant target regions from the drop down list.
- QC for Targeted Sequencing Set the Minimum coverage parameter of the QC for Targeted Sequencing tool. Using default settings, samples where 90 percent of target region positions do not meet this threshold will be flagged in the sample report generated by the workflow.
- Create Sample Report Select relevant summary items and specify thresholds for quality control. Summary items, thresholds and an indication of whether specified thresholds were met, will be shown in the quality control section of the sample report. The default summary items are appropriate for many data sets, but may need to be adjusted. For additional information, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Create_Sample_Report.html.
- Result handling Choose if a workflow result metadata and/or log should be saved.
- Save location for new elements Choose where to save the data, and press Finish to start the analysis.
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