Assembly of genomes with Hifiasm and Masurca

Example of hifiasm assembly with HiFi and HIC data

hifiasm -o genome.asm -t64 --h1 hic-reads1.fastq.gz  --h2 hic-reads2.fastq.gz hifi.fastq.gz

This command will produce the assemblies for haplotypes two files:

• genome.asm.hic.hap1.p_ctg.gfa
• genome.asm.hic.hap2.p_ctg.gfa

And merged genome will be saved in:

• genome.asm.hic.p_ctg.gfa

The *.gfa files can be converted to FASTA with the following command: awk '/^S/{print ">"$2;print $3}' genome.asm.hic.p_ctg.gfa > genome.asm.fa

Chromosome scaffolding with MaSuRCA

chromosome_scaffolder.sh -t 64 -r chm13v2.0.fa -q genome.asm.fa -s hifi.fastq.gz -ch 50

The scaffolded genome will be saved in *.reconciled.fa file