Pacific Biosciences
Tertiary analysis for HiFi long-read sequencing, including the PureTarget Carrier Pipeline (PTCP) integrated into the VarSeq Suite for carrier screening across 20 clinically actionable genes.
HiFi long-reads in your VarSeq tertiary workflow
As a member of the PacBio Partner Program, Golden Helix provides tertiary analysis tools for HiFi long-read sequencing. Your lab imports PacBio variant calls into VarSeq for annotation, ACMG/AMP classification, filtering, and clinical reporting, alongside the short-read workflows you already run.
The integration covers SNVs, indels, structural variants, copy-number changes, and the variant classes HiFi data uniquely surfaces: phased haplotypes, tandem repeat expansions, and methylation in targeted regions. Each variant class lands in one VarSeq project, where it can be integrated into a clinical report.
PureTarget Carrier Pipeline, integrated into the Golden Helix suite
PacBio PureTarget is an amplification-free, CRISPR-Cas9 target enrichment assay that sequences DNA on Revio (SPRQ) and Vega systems. The PureTarget Carrier Panel covers 20 clinically relevant genes for recessive-disease carrier screening, including SMN1/SMN2, CYP21A2, GBA, HBB, FMR1, FXN, F8, and RPGR. Golden Helix runs the PureTarget Carrier Pipeline (PTCP) on the same platform that hosts your VarSeq projects, with annotation, classification, and reporting handed off in one place.
SNVs & Indels
Phased small variants from HiFi reads aligned with pbmm2.
Tandem Repeats
TRGT genotyping sizes long expansions and sequences interruption motifs (e.g., FMR1, FXN).
Structural Variants
Sawfish-called inversions and large deletions in target regions, scored per ACMG/ClinGen 2019.
Paralogs
Paraphase resolves SMN1/SMN2, CYP21A2/CYP21A1P, and other segmental-duplication paralogs.
PTCP modules running in the suite
The Golden Helix integration runs the same five PTCP stages PacBio publishes on GitHub, configured to feed VarSeq directly. Your team starts from PacBio HiFi BAMs and ends with a VarSeq project ready for ACMG classification.
HiFi BAM alignment
Tandem repeat genotyping
Gene-paralog resolution
Structural variant calling
Coverage & metrics report
Variant classes short-read carrier panels miss
Paraphase phases the highly similar SMN1/SMN2 paralogs from HiFi reads, so your lab calls SMA carrier status without an orthogonal MLPA assay.
TRGT sizes long CGG and GAA tandem expansions and reads through interruption motifs that throw off short-read assemblies.
21-hydroxylase deficiency calls disambiguated from the CYP21A1P pseudogene and surrounding RCCX rearrangements.
PureTarget Carrier Report sample
Click the preview to open a sample PureTarget Carrier report. It includes the variant summary, tandem-repeat genotypes, per-locus motif and read-depth detail, and the primary findings page, supported by visualizations and citations.
Download PDFNote: the example report can be customized to match your lab's branding, content preferences, and layout. This is a sample only and should not be used for clinical decision-making.
Reference Resources
PacBio PureTarget
CRISPR-Cas9 amplification-free target enrichment for HiFi sequencing. Carrier panel, repeat-expansion panel, and custom controls.
PureTarget Carrier Pipeline (PTCP)
Open-source PacBio pipeline that orchestrates pbmm2, TRGT, Paraphase, Sawfish, and ptcp-qc. Golden Helix runs it inside the suite.
Run PureTarget Through ACMG Reporting
See your lab take PacBio HiFi PureTarget data through PTCP and into a sign-off-ready VarSeq carrier-screening report.