Zhigui Bao

Output unsorted SAM

3

Hi, Haowen Chromap is super fast when I use pair format. But I want to use chromap for assembly scaffolding pipeline (chromap + yahs), espeically for large plant genome. Since...

Bézier curve for synteny block

2

Hi, @thackl Can `gggenomes` use the Bézier curve for synteny block ? Like the sankey plot https://github.com/davidsjoberg/ggsankey 

Adding wfmash as alinger

2

Hi, Alonge Can `RagTag` add `wfmash` as alinger? It also ouput the paf file and is much faster than minimap2 or nucmer on high repitive plant assemblies.

Hi, @thegenemyers Can fastk use the `pigz` for parallel gzipping large fastq?

Hi, I installed MoltenVK and Vulkan on M1 Mac and `gfaestus` cargo building seems very smooth. But when I run the `gfaestus` with my graph, it display was all black...

empty pickle for self mapping

1

Hi, @tjiangHIT If I used `cuteSV` to validate the genome assembly error (HiFi reads mapping back to the assembly itself). Some pickles will be empty, but `cuteSV` will report errors...

Hi, When I use `SVision` for plant reads-based SV calling, there is some warning. I see this may due to the cluster busy when another task running. It stock more...

Can Dinvestigate sliding window by length not SNP number

2

Hi, @millanek Can Dinvestigate sliding window by length (such as vcftools, 25kb window, 10kb step)? Zhigui Bao

Hi, @lh3 `Dipcall` is designed for the diploidy, can I use the rule in the makefile for handling a plant tetraploidy genome? ``` bash # mapping for hap in `seq...

Filter out very long intron gene (max intron size)

6

Hi, @lh3 It seems a lots of long-intron protein mapping in the `miniprot` result, can we use some parameters to filter out these? Its size smaller than the default `-G`...