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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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After adjusting the parameters based on the information from the Hifiasm.log file, the issue of "phased assembly is much larger than the estimated genome size" still persists. #582

Open xujialupaoli opened 9 months ago

xujialupaoli commented 9 months ago

Hello, When assembling the genome of a species using HiFi data with hiFiasm, I encountered a peculiar situation. The genome size of my species is approximately 1.1 G. Following your software recommendations and based on the k-mer analysis results from the log file, we set the parameters as -s 0.35 --hom-cov 24. However, the output assembly results show two haplotypes with sizes of 5.3 G and 5.4 G, respectively. I hope you can help me understand why this is happening and how to address it effectively.

My command hifiasm -o /home/work/enlian/hifiasm_result_5_onlyhifi/5_hifiasm_ONHF -t 64 -s 0.35 --hom-cov 24 /home/work/enlian/m84114_231110_103510_s2.hifi_reads.bc2059.fq /home/work/enlian/m84114_231113_054910_s2.hifi_reads.bc2059.fq /home/work/enlian/m84114_231121_083911_s1.hifi_reads.fastq

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hifiasm_ONHF.txt

chhylp123 commented 9 months ago

Do you know the homozygous coverage of your dataset? By looking at the k-mer plot, the main issue is that the dataset is not so clean around 2 or 3. A good k-mer plot should like https://hifiasm.readthedocs.io/en/latest/faq.html#why-does-hifiasm-stuck-or-crash.