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hifi-assembly

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Assembles haplotype-resolved diploid and telomere-to-telomere (T2T) genomes from PacBio HiFi reads with hifiasm (HiFi-only, Hi-C, or trio phasing) and verkko (HiFi + ultralong ONT for T2T), extracting contigs from GFA and routing phasing QC to k-mer/trio metrics. Covers why a primary assembly is a haplotype mosaic that exists in no cell, partial-vs-full phasing (the .bp. vs .dip. filename convention), the purge-default trap on inbred samples, the --hom-cov coverage-estimate alarm, and verkko-vs-hifiasm for T2T. Use when assembling a diploid eukaryote from HiFi, phasing haplotypes with parents (trio) or Hi-C, deciding whether to chase T2T, or diagnosing switch errors invisible to N50/BUSCO/QV.

When to use

• assembling a diploid eukaryote from HiFi
• phasing haplotypes with parents (trio)
• phasing haplotypes with Hi-C
• deciding whether to chase T2T
• diagnosing switch errors invisible to N50/BUSCO/QV
• building two cleanly phased haplotypes
• T2T-grade assembly with HiFi + ultralong ONT

When not to use

• haploid representation for rough gene location
• allele-aware analysis on primary mosaic assemblies

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