bio-genome-assembly-hifi-assembly

name	bio-genome-assembly-hifi-assembly
description	High-quality genome assembly from PacBio HiFi reads using hifiasm with phasing support. Use when building reference-quality diploid assemblies from HiFi data, especially with trio or Hi-C phasing for fully resolved haplotypes.
tool_type	cli
primary_tool	hifiasm

HiFi Assembly

Basic Assembly

# Primary assembly (single haplotype consensus)
hifiasm -o output_prefix -t 32 reads.hifi.fastq.gz

# Output files:
# output_prefix.bp.p_ctg.gfa  - Primary contigs
# output_prefix.bp.a_ctg.gfa  - Alternate contigs
# output_prefix.bp.hap1.p_ctg.gfa - Haplotype 1 (if phased)
# output_prefix.bp.hap2.p_ctg.gfa - Haplotype 2 (if phased)

# Convert GFA to FASTA
awk '/^S/{print ">"$2;print $3}' output_prefix.bp.p_ctg.gfa > assembly.fasta

Trio-Binned Phasing

# With parental short reads for trio binning
hifiasm -o trio_asm -t 32 \
    -1 paternal.yak \
    -2 maternal.yak \
    child.hifi.fastq.gz

# Create yak databases from parental Illumina reads first
yak count -b37 -t16 -o paternal.yak paternal_R1.fq.gz paternal_R2.fq.gz
yak count -b37 -t16 -o maternal.yak maternal_R1.fq.gz maternal_R2.fq.gz