QIAseq xHYB Long Reads to Germline Variants (ONT) (beta)
The QIAseq xHYB Long Reads to Germline Variants (ONT) (beta) template workflow can be used for analyzing Oxford Nanopore data produced with QIAseq xHYB Long Read Panels.
Note: The workflow is in beta. It is under active development and subject to change without notice. Generated results may not be accessible when later versions of the plugin are installed.
The workflow includes all necessary steps for processing and analyzing the reads:
- Reads are mapped and variants are called using LightSpeed Long Reads to Germline Variants (beta), see LightSpeed Long Reads to Germline Variants (beta).
- Structural variants are called using Structural Variant Caller for Long Reads.
- Variants are annotated with amino acid changes using Genotype Track Amino Acid Changes (beta), see Genotype Track Amino Acid Changes (beta).
- Target coverage statistics are generated using QC for Targeted Sequencing.
- A summary report is created using Create Sample Report.
Launching the workflow
To run the workflow, go to:
Template Workflows | LightSpeed Workflows (
) | QIAseq workflows (
) | QIAseq xHYB Long Read (
) | QIAseq xHYB Long Reads to Germline Variants (ONT) (beta) (
)
For general information about launching workflows, see Launching workflows individually and in batches.
Options can be configured in the following dialogs:
- 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 xHYB Long Read Panels hg38 will be pre-selected 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.
The QIAseq xHYB Long Read Hereditary Cancer Panel includes a target region for GSTT1 on chr22_KI270879v1_alt, that is not in the hg38 no alt reference sequence.
If the QIAseq xHYB Long Read Panels hg38 reference data set does not contain the needed 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.
- Target regions Choose the relevant target regions from the drop down list.
- LightSpeed Long Reads to Germline Variants (beta)
Specify options for the LightSpeed Long Reads to Germline Variants (beta) 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.
- 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).
- 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.
- 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.
Subsections