For Hi-C mode, issues about the use of "-l 0" and the number of homozygous bases.

[qdu-beep]

Dear Hifiasm community and developers，

I'm using hifiasm 0.19.7-r598 and I'm having some problems. I have searched through the software's documentation and online forums, but unfortunately, I'm not sure how to solve the problem correctly. Therefore, I kindly request your assistance in guiding me on how to rectify this problem.

The two haplotype files I got differed a lot in size. It seems that the peak value is correct, should I use the -s parameter? I'm rather new to the field, so please bear with me if this is an uninformed question. Also, I have another question. I don't quite understand what the number of heterozygous bases and the number of homozygous bases mean?

1. my command： hifiasm -l 0 -o glauca.asm -t 48 --h1 /control2/FDHC230012121-1A_L1out_1.fq.gz --h2 /control2/FDHC230012121-1A_L1out_2.fq.gz genome.fastq

2. Some important output information：

3. my log: hifiasm.txt

I truly appreciate your willingness to help. May your days be filled with happiness! @chhylp123

[qdu-beep]

When I didn't use "-l 0", I got two haplotype files of about the same size. In particular, the heterozygous bases and the number of homozygous bases are very different from that obtained when using the -l 0 parameter. Is this due to some clear repetitions being performed by default? I don't quite understand, I hope you don't mind my wrong idea. with "-l 0" : The number of heterozygous bases is much greater than that of homozygous bases. withou "-l 0" : The number of homozygous bases is much greater than that of heterozygous bases. Please refer to these figures:

[chhylp123]

Please do not use -l0 since it is designed to assemble homozygous genomes.

[qdu-beep]

Thank you very much for your help! The samples used for sequencing were derived from selfing. However, currently it is not possible to perform genome survey analysis due to the lack of illumina reads. Based on the results, I think our genomes are indeed not homozygous.

I would like to confirm again whether the results I get by running hifiasm based on the previous bin file using default parameters are correct? Because I don't know how to understand the number of heterozygous bases and the number of homozygous bases in the log file. In addition, from the kmer diagram, there is only one peak, and "peak_hom:20;peak_het:-1" seems to be a wrong prompt (from the previous issue).

Thanks for your answer!