Yumin Huang

The parameters for heterozygous plant genome

1

Hello, We used hifiasm for a heterozygous plant genome assembly. We have estimate the basic information about this genome using NGS data with GCE analysis: heterozygous ratio is about 1.36%...

giraffe performance

10

Hello, I encountered the following warning while running the Vg Giraffe workflow: ``` ...... Not counting CPU instructions because perf events are unavailable: No such file or directory warning[vg::Watchdog]: Thread...

json format

3

Hi, I am using `vg view -aM filtered.gam` to view the output file of the aligments, I try to interpret the json format. I know some basic concepts, such as...

MSA input and handling mixed ploidy species in NetRAX

2

Hello, and thank you for developing and maintaining NetRAX. I'm interested in using NetRAX to infer phylogenetic networks for a group of species. However, I am still quite new to...

vg autoindex input vcf

9

I‘d like to know whether [vg autoindex](https://github.com/vgteam/vg/wiki/Mapping-short-reads-with-Giraffe) can accept vcf files of polyploid genotypes as input? Something like this: ``` 0/0/0/0/1/1/1/1/1/1:38:17,21:17:629:21:777 ``` I tried running it and the result was...