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Dear VG Team Members,
I hope this message finds you well.
While using the vg giraffe tool to align short reads, I encountered an issue similar to the one described in issue #4171 . Specifically,…
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Hi,
now that hifiasm 'generates a pair of haplotype-resolved assemblies', what is the best way of scaffolding these? This has been on my mind a bit lately, and this might not be the best place to ask…
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Hello guys,
I tried compiling shapeit4.2 on Debian 11 using both g++ 10.2.1 20210110 and g++ 9.3.0 though I am getting a similar error.
g++ 10.2.1 20210110
```
pietro@cookbox:~/shapeit4$ make…
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Hello,
I am trying to install Haploclique (on Ubuntu) and I always get the same error message:
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CMake Warning at external/googletest/googletest/CMakeLists.txt:51 (project):
VERSION keyword…
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Hi
I am working on assembling a genome using hifiasm, and I obtained a phased assembly (hap1). However, the size is bigger than I expected and it has a high degree of duplication per BUSCO. I am su…
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Since you guys have run `Herro` or perhaps `dorado correct`, I thought that perhaps this github issue might be of interest https://github.com/nanoporetech/dorado/issues/851 that during the minimap2 al…
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Hi!
Can CHOP be used to do the actual read mapping, or does it just create a fasta file that I e.g will need to index with BWA and then map reads to? If so, I assume my final alignments will be rel…
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Dear Hifiasm team,
thank you very much for introducing this feature of HiC mode on hifiasm. Before I was running SALSA after assembly.
I want to know what would be the easiest way to make the hic …
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It seems that the genotype likelihood calculation used by HaplotypeCaller ends up double-counting fragment evidence when the variant is covered by both reads in a read pair. For a homozygous call, thi…
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Hi, I used FastANI for several plant genome and did get results. The ANI values were higher for species with closer genetic relationship. But I am not sure if the ANI values meaningful?
Thanks a lot …