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Hi, may I ask a question: merqury provides phased block N50, it seems it does not provide phased block NG50, is it right or I missed something? Thanks in advance.
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Hi, I assembled the genome of allotetraploid species using hifiasm with size of ~3.7gb. I used the PacBio HiFi reads in Merqury for kmer analysis of genome estimation of our allotetraploid species. I …
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Hi,
When I use PloidyPlot, I get these errors,
PloidyPlot -T4 fastk
sh: Logex: command not found
PloidyPlot: Something went wrong with command:
Logex -T4 '.trim=A[4-]' fastk
and
"Kat…
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HI Arang,
One question I have is that I used hifi data on well assembled T2T genomes to predict QV and found in QV between 53-56(Completeness:93). And I found other genomes that are not T2T, some p…
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Hi,
I am not sure about this issue as I am using a non-standard installation of FastK (https://github.com/davebx/FASTK/commit/305d01b81204f6870c034b9abd9d8c280d4d4b76), but maybe it applies to the …
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IPA produces:
- `*.purged.haplotigs.fasta`
- `*.purged.primary.fasta`
HiFi asm produces:
- `*.bp.hap1.p_ctg.{fasta,gfa}`
- `*.bp.hap2.p_ctg.{fasta,gfa}`
- `*.bp.p_ctg.{fasta,gfa}`
- `*.bp.p_u…
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Hi,
How to limit threads when running merqury (merqury.sh)? I used default parameter and it seemed to take up too many cores.
I'll really appreciate your suggestions.
Thanks.
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Hi,
I successfully assembled an _A. thaliana_ genome for which I obtained two partially phased haplotypes of size 148.1 Mb (hap1) and 146.4 Mb (hap2), respectively. These files are in **.fasta** f…
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Hi,
I assemble a genome using Hifi reads. However, I am confused that NGS reads and Hifi reads which might be better for qualifying our genome. I thinks NGS reads will be biased on high GC and repet…
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Hello,
I am writing here as I could not find a google group for yahs. This is not a software issue, more of an unexpected behaviour in my data I could use help interpreting.
I am working with Pa…