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Hi there,
Do you recommend to polish hifi assemble results (like hifiasm or hicanu results) ? And why ?
Best,
Kun
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Hi,
I meet a similar error, hope you can give me some advise.
The estimated haploid genome size was ~1G. I get ~40G hifi reads (ccs) with 3 times (10G+10G+10G).
I can run hifiasm and…
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Hi Yoshi,
I noticed that slightly different k-mer coverage histograms are plotted 5-times in the hifiasm.log: what is the significance? I didn't find explanation in the hifiasm documentation but it a…
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What is the best way to generate hifiasm-like primary contigs from the results of verkko? For reference, we generated an assembly with only HiFi reads because we don't have ONT reads. I saw #59 and I …
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Our Slurm cluster enforces memory usage with cgroups. I added `--mem=32G` as a default to the snakemake profile. This is of course not good enough as it is too high for certain steps and too low for t…
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Hi, I've recently assembled a human genome using a set of HiFi FASTQs and the results look great. However, when another group tried to reproduce the genome assembly, we noticed a very minor difference…
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I am sorry for being a fresh learner. I just want know in what file haplotype information should be present.
Right now, I have fasta files below:
AJ.hap1.fa
AJ.hap1.fa.fai
AJ.hap1.fa.stats
AJ.h…
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Hi
I am trying to scaffold two separate phased haplotype assemblies of the same diploid plant genome (assembled with HIFIasm). For that, I am using the same HiC data for the scaffolding process of…
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Hi! I wonder what _1, _2 mean? eg. HG002_1.bed and HG002_2.bed. Do they represent the results from two haplotypes?
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Hi,
We used hifi reads(30G) and ont(20G) reads for a plant (genome size ~500m).
While the hifiasm's output seems to be reasonable, about 550m; the verkko's results seems to be weird.
First I used …