WGS on single cells with BioScryb and Qiagen kits

BioScryb kit: ResolveDNA Library Preparation Kit Qiagen kit: QIAseq Repli-G Single Cell DNA Library Kit

Samples

• Qiagen:
  • 10 st single cell (MM1S)
  • 1 st mini-bulk, 10 cells (MM1S)
  • 1 st positive control DNA (mouse)
• BioScryb:
  • 10 st single cell (MM1S)
  • 1 st mini-bulk, 10 cells (MM1S)
  • 1 st positive control DNA (mouse)

Directory organization

• analysis: Analysis results and run files.
  • basejumper: Reports and Ginkgo CNV calls generated using BioSkryb BaseJumper platform
  • copykit: CNV analysis with copykit
  • downsample_40M: Analysis on samples downsampled to 40M reads.
    • downstream: Downstream library quality analysis
    • sarek_GRCh38: Genome alignment and QC using nf-core/sarek
  • downsample_qc: Analysis on samples downsampled to 40M reads.
    • downstream_qc: Downstream library quality analysis
    • sarek_GRCh38: Genome alignment and QC using nf-core/sarek
  • qiagen_repli_g_full: Analysis on Qiagen samples without downsampling.
    • downstream: Downstream library quality analysis
    • sarek: Genome alignment and QC using nf-core/sarek
• data: Sequencing data generated for project.
  • P33410: Raw FASTQS (soon available on ENA)
  • P33410_downsampled Downsampled FASTQs and run files for this generation
• reports: HTML reports and Jupyther notebooks related to different steps of analysis
• resources: Resource files related to analysis
  • PacBioHiFi_pr_023_003_MM1S_hificnv: PacBio HiFi data HiFiCNV calls and coverage files
• scripts: Scripts related to analysis

Links

Genstat project: G.Applications_24_11, P33410 Google drive: GA_24_01