Hello,
I am working on a diploid organism with a 12Gbp expected genome size and different heterozygosity levels.
I have been doing some hifi assemblies with Hifiasm (V0.19), my first primary and haplotype-resolved assemblies were great (1,2,3,4,6 and 8). N50 values were also similar, however recently, new assemblies had a lot of missing and duplicated Buscos (5-7- and TF) even though I am using the same Hifiasm version. Primary assemblies had duplicated Buscos and haplotype-resolved assemblies had many missing Buscos.
Hello, I am working on a diploid organism with a 12Gbp expected genome size and different heterozygosity levels.
I have been doing some hifi assemblies with Hifiasm (V0.19), my first primary and haplotype-resolved assemblies were great (1,2,3,4,6 and 8). N50 values were also similar, however recently, new assemblies had a lot of missing and duplicated Buscos (5-7- and TF) even though I am using the same Hifiasm version. Primary assemblies had duplicated Buscos and haplotype-resolved assemblies had many missing Buscos.
The common commands that I was using are;
hifiasm -o $work_dir/l0.asm -t 32 -l0 $work_dir/*.fastq.gzhifiasm -o $work_dir/l3.asm -t 32 -l3 $work_dir/*.fastq.gzBusco scores of all assemblies;
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Genome ID | Primary assembly | Haplotype 1 | Haplotype 2 -- | -- | -- | -- 787-1 | C:97.5%[S:69.6%,D:27.9%],F:0.4%,M:2.1%,n:5366 | C:96.5%[S:87.7%,D:8.8%],F:0.5%,M:3.0%,n:5366 | C:93.4%[S:87.6%,D:5.8%],F:0.4%,M:6.2%,n:5366 787-2 | C:97.6%[S:93.4%,D:4.2%],F:0.3%,M:2.1%,n:5366 | C:96.5%[S:92.4%,D:4.1%],F:0.3%,M:3.2%,n:5366 | C:92.0%[S:87.7%,D:4.3%],F:0.4%,M:7.6%,n:5366 787-3 | C:97.4%[S:91.8%,D:5.6%],F:0.4%,M:2.2%,n:5366 | C:77.8%[S:74.2%,D:3.6%],F:0.7%,M:21.5%,n:5366 | C:59.4%[S:57.4%,D:2.0%],F:0.8%,M:39.8%,n:5366 787-4 | C:97.5%[S:86.5%,D:11.0%],F:0.4%,M:2.1%,n:5366 | C:96.4%[S:91.1%,D:5.3%],F:0.4%,M:3.2%,n:5366 | C:84.1 [S:80.2%,D:3.9%],F:0.4%,M:15.5%,n:5366 787-6 | C:97.4%[S:90.6%,D:6.8%],F:0.4%,M:2.2%,n:5366 | C:96.0%[S:91.5%,D:4.5%],F:0.4%,M:3.6%,n:5366 | C:82.8%[S:78.8%,D:4.0%],F:0.4%,M:16.8%,n:5366 787-8 | C:97.6%[S:85.3%,D:12.3%],F:0.3%,M:2.1%,n:5366 | C:96.7%[S:90.6%,D:6.1%],F:0.4%,M:2.9%,n:5366 | C:95.4%[S:90.7%,D:4.7%],F:0.3%,M:4.3%,n:5366 787-7 | C:97.6%[S:73.7%,D:23.9%],F:0.3%,M:2.1%,n:5366 | C:77.4%[S:69.9%,D:7.5%],F:0.7%,M:21.9%,n:5366 | C:61.8%[S:58.2%,D:3.6%],F:0.6%,M:37.6%,n:5366 787-5 | C:97.6%[S:77.7%,D:19.9%],F:0.3%,M:2.1%,n:5366 | C:81.3%[S:75.3%,D:6.0%],F:0.4%,M:18.3%,n:5366 | C:64.6%[S:62.0%,D:2.6%],F:0.6%,M:34.8%,n:5366 TF | C:97.6%[S:86.5%,D:11.1%],F:0.3%,M:2.1%,n:5366 | C:82.9%[S:78.5%,D:4.4%],F:0.5%,M:16.6%,n:5366 | C:64.9%[S:62.2%,D:2.7%],F:0.5%,M:34.6%,n:5366