Trio-binning Assembly

When parental short reads are available, hifiasm can also generate a pair of haplotype-resolved assemblies with trio binning. To perform such assembly, you need to count k-mers first with yak and then do assembly:

yak count -k31 -b37 -t16 -o pat.yak paternal.fq.gz
yak count -k31 -b37 -t16 -o mat.yak maternal.fq.gz
hifiasm -o NA12878.asm -t 32 -1 pat.yak -2 mat.yak NA12878.fq.gz

Here NA12878.asm.hap1.p_ctg.gfa and NA12878.asm.hap2.p_ctg.gfa give the assemblies for two haplotypes. In the binning mode, hifiasm does not purge haplotig duplicates by default. Because hifiasm reuses saved overlaps, you can generate both primary/alternate assemblies and trio binning assemblies with:

hifiasm -o NA12878.asm --primary -t 32 NA12878.fq.gz 2> NA12878.asm.pri.log
hifiasm -o NA12878.asm -t 32 -1 pat.yak -2 mat.yak /dev/null 2> NA12878.asm.trio.log

The second command line will run much faster than the first. The phasing switch error rate and hamming error rate are able to be evaluated quickly by yak:

yak trioeval -t16 pat.yak mat.yak assembly.fa

The W-line and H-line reported by yak trioeval indicate switch error rate and hamming error rate respectively:

W       26714   3029448 0.008818
H       24315   3029885 0.008025

For this example, the switch error rate is 0.8818% and the hamming error rate is 0.8025%. If the hamming error rate or the swith error rate of trio-binning assembly is very high, it might be caused by hifiasm or the incorrect parental data. To fix it, see Why the hamming error rate or the swith error rate of trio-binning assembly is very high? for more details.