bio-genome-assembly-hifi-assembly

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

## Use Hi-C reads for phasing (no parents needed)

hifiasm -o hic_asm -t 32 \
    --h1 hic_R1.fastq.gz \
    --h2 hic_R2.fastq.gz \
    reads.hifi.fastq.gz