Research Use Only (RUO) Assays

Shallow Whole Genome (sWGS)

../_images/shallow-pipeline.png

Fig. 7 Shallow Whole Genome Analysis Pipeline

  1. The shallow whole genome pipeline commences once the bcl2fastq workflow is completed and FASTQ files are available.

  2. FASTQ files are quality controlled using FastQC. FastQC produces quality control metrics related to reads (e.g. total numbers of reads)

  3. FASTQ files are aligned with BwaMem2 to generate an unprocessed lane-level BAM file.

  4. Data is quality controlled with the bamQC workflow generating a JSON file of alignment QC metrics for review. The quality control metrics include the insert size distribution, amount of duplication, mapping percentage, and other WG ‘Single Lane’ metrics described in QM. Quality Control and Calibration Procedures.

  5. The BAM files are processed with ichorCNA to estimate tumour fractions in ultra-low pass whole genome sequencing (WGS) and prediction of large-scale copy number variation (CNV).

  6. All alteration files are provided to Djerba to generate a provisional clinical report for review by genome interpreters.

sWGS Workflows and Software

  • Human Genome Reference: hg38-p12
Table 18 Shallow Whole Genome Sequencing Software

Workflow

Version

Parameterization

Reference Data

Bioinformatics Software

bcl2fastq

3.1.3

vidarr-u20-bcl2fastq.shesmu

barcodex-rs/0.1.2 bcl2fastq-jail/3.1.2b bcl2fastq/2.20.0.422

bwamem2

1.0.1

vidarr-u20-bwamem2.shesmu

hg19-bwamem2-index/2.2.1 hg38-bwamem2-index-with-alt/2.2.1

barcodex-rs/0.1.2 python/3.7 slicer/0.3.0 rust/1.45.1 cutadapt/1.8.3 bwa-mem2/2.2.1 samtools/1.9

crosscheckFingerprintsCollector

1.1.0

vidarr-u20-crosscheckFingerprintsCollector_fastq_exceptions.shesmu vidarr-u20-crosscheckFingerprintsCollector_bam.shesmu vidarr-u20-crosscheckFingerprintsCollector_fastq.shesmu

hg38-star-index100/2.7.3a hg19-bwa-index/0.7.17 hg19-star-index100/2.7.3a hg38-bwa-index-with-alt/0.7.17

samtools/1.15 crosscheckfingerprints-haplotype-map/20230324 tabix/0.2.6 seqtk/1.3 star/2.7.3a bwa/0.7.17 gatk/4.1.6.0 samtools/1.14 gatk/4.2.0.0 samtools/1.9

dnaSeqQC

1.1.0

vidarr-u20-dnaseqqc.shesmu

hg19-bwa-index/0.7.12 hg38-bwa-index/0.7.12 mm10-bwa-index/0.7.12

bwa/0.7.12 mosdepth/0.2.9 bam-qc-metrics/0.2.5 slicer/0.3.0 python/3.6 cutadapt/1.8.3 picard/2.21.2 samtools/1.9

fastqc

3.2.0

vidarr-u20-fastqc.shesmu

java/11 fastqc/0.11.9 perl/5.28

ichorcna

1.2.0

vidarr-u20-ichorcna.shesmu

hg19-bwa-index/0.7.12 hg38-bwa-index-with-alt/0.7.12

python/3.6 hmmcopy-utils/0.1.1 samtools/1.14 bwa/0.7.12 pandas/1.4.2 bam-qc-metrics/0.2.5 mosdepth/0.2.9 ichorcna/0.2 picard/2.21.2 samtools/1.9

Change Log

  • June CR-119 update (#14) by Morgan Taschuk at 2026-07-21 19:22:33

    * Remove references to mini-Djerba * Improve changelogs by pulling in the actual changes for each page with sphinx-git

  • Update tar assay to 4.0; move shallow whole genome to RUO pipelines s… (#4) by Morgan Taschuk at 2025-10-23 20:04:08

    …ection

  • Update tar assay to 4.0; move shallow whole genome to RUO pipelines section by Morgan Taschuk at 2025-10-16 18:59:56