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Dear all,
I'm here for the first time in the community and have been trying for some time to obtain a pangenome to use as a reference for mapping short reads using `vg giraffe` and subsequent varia…
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Hi
I've been running Cactus on 3 different Barley genomes (planning to scale up to more genomes later). I've been running each job to create alignments of each chromosome from 1 to 7. I'm breaking …
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(I originally thought this had to do with `inject`, but it has more to do with `build`. I have removed my original comment but am keeping the issue open because the discussion below is still valuable.…
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Hi,
Up until now I've been running cactus in singleMachine mode, but now decided to try the cluster option. I've set the TOIL_SLURM_ARGS to a set that I normally use with Slurm batch jobs, but the p…
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I have test a small set of 2 maize genomes (B73 and Mo17) according to the pangenome pipeline
However, when I try to align each chromosome with Cactus, It comes to an error.
The command I have made…
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Hi,
I have induced a graph genome from three human genomes with minimap2 (-x asm20) and seqwish.
I have removed any alignments smaller than 100kb.
The three genomes are hg19, and the two haplotype…
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Hello,
Many users of PanGenie might wish to use vg giraffe to align reads for short-variant calling, but use PanGenie for structural variant calling.
Inspired by PanGenie, the new haplotype-bas…
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**1. What were you trying to do?**
Mapping Illumina WGS data to a cactus-minigraph pangenome.
In case it is relevant, the pangenome was constructed with 5 marsupial genomes, which have a few lon…
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Hi,
I only have two genome and I want to build a graph via cacuts. But a tree is needed for cactus. How can I construct tree based on two genome (maybe I cann't build tree contained two genome)?
…
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Hello,
I've been mapping paired end reads to a graph built with minigraph-cactus
```
vg giraffe --progress --fragment-mean $frag_mean --fragment-stdev $frag_stdev -Z ${inDir}/arenosa_pg.d2.gbz …