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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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tetraploïd assembly, missing kmers in p_utg and r_utg files #616

Open chklopp opened 7 months ago

chklopp commented 7 months ago

I'm trying to assemble a tetraploïd genome with hifiasm 0.19.8 using the --n-hap 4 option. But when I check the assembly kmer content there are many missing kmers even when I merge hap1 and hap2. Therefore I checked also the unitig files. Which also show missing kmer mers http://genoweb.toulouse.inra.fr/~klopp/fqsdfkjhqskljfhqiurhqeuihfsjh/hifiasm_0.19.8_no_HiC.bp.r_utg-main.mx.spectra-cn.png http://genoweb.toulouse.inra.fr/~klopp/fqsdfkjhqskljfhqiurhqeuihfsjh/hifiasm_0.19.8_no_HiC.bp.p_utg-main.mx.spectra-cn.png

Are their other options I should use to improve the assembly kmer content?