kass

kass assembles and annotates diploid human KIR (natural killer-cell immunoglobulin-like receptor) haplotypes from targeted long-read sequencing data using IDT xGen Lockdown probe capture and PacBio HiFi reads.

Key Features:

• Targeted probe capture: Uses IDT xGen® Lockdown probes for hybridization capture of KIR region fragments.
• Fragment size: Captures 2–8 kb sheared DNA fragments for long-read sequencing.
• Long-read sequencing: Utilizes PacBio HiFi reads generated on a PacBio Sequel system.
• Error correction and binning: Applies error correction and read binning prior to assembly.
• Assembly: Assembles KIR haplotypes with the Canu assembler.
• Phasing: Produces fully phased diploid KIR haplotypes.
• Annotation: Includes gene locations and exon/intron boundary annotation within the workflow.
• Validation metrics: Demonstrated assemblies covering 97% of the GenBank reference with 99.97% concordance and 1.8 haplotigs required to cover 75% of the reference.

Scientific Applications:

• Haplotype sequencing and phasing: Enables complete sequencing and phasing of all diploid human KIR haplotypes.
• Population-scale studies: Facilitates large-scale analysis of KIR genetic variation across populations.
• Clinical genotyping: Supports clinical applications requiring high-resolution KIR haplotype information.
• Benchmarking and validation: Validated against long-range fosmid library sequencing as a ground truth for accuracy assessment.

Methodology:

Error correction and read binning of PacBio HiFi data followed by assembly with Canu and annotation of gene locations and exon/intron boundaries.