DipGenie v2.0

DipGenie v2.0 infers the two haplotypes of a diploid genome from a pangenome graph using paired-end short reads, Hi-C reads, or both, scoring read coverage and linkage jointly.

What's new

• Linkage-aware inference (FDPI): coverage and short-read/Hi-C/panel linkage are optimized together under a recombination budget.
• Hi-C support for orienting phase blocks along whole chromosomes.
• Acyclic and cyclic graphs (GFA v1.1, P/W lines) and phased VCF panels, with a reusable index.
• Built-in variant calling: phased VCF output with no external tools at run time.
• Multi-chromosome panels; identical results for any number of threads.

Changes from v1

• New command line; diploid inference only.
• Paired-end reads only.
• VCF panels are read directly.