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My command:
`/usr/bin/time -v -o time.log cactus-pangenome ./js $ref.pangenome.list --outDir ./$ref.pangenome --outName $ref.pangenome --reference $reference --vcf --filter $N --haplo --giraffe cli…
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Dear seqwish team,
I built a bacteria pangenome graph with wfmash+seqwish+bandage, which is from Chlamydia trachomatis species, about 50 genomes/strains with ANI> 99%, I have the attached graph out…
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Hi guys,
A number of additional scripts are provided (in the scripts and tools directories) for converting or analysing the PIRATE outputs.
I am using the ones to convert and run treeWas (pangenom…
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Hi,
In the output VCF of MC pipeline, there are a few duplicated variants after left-algin. Below is one example from the HPRC VCF:
Before left-align (`bcftools view -r chr22:15409352-15409435 h…
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Hello,
I am trying to build a pangenome using pig data from multiple breeds. The input data is 4.5GB when compressed, and I am using the Docker image ghcr.io/pangenome/pggb:latest.
I ran the follo…
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Hello,
I am running ppanggolin on about 40K species, on a slurm managed cluster, and after some time the multi-threaded processes hang indefinitely.
My initial thinking was that the total memory …
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Hi, I want to a create pangenome plot for bacteriophages with **phylogenetic tree** (left side) + **gene presence/absence** (right side) + **gggenome plot that has all ORFs/CDS** (in top of presence/a…
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I ran PIRATE with 322 genomes (gff files) as input, but the file indicates 321 genomes. Is there any way to investigate why the count decreased from 322 to 321? The confirmation details are as follow…
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I've been closely following your recent paper on graph augmentation, which I find quite intriguing. However, I have a few questions. Could you elaborate on the advantages of choosing to augment a pang…
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First of all, I'd like to thank you for the amazing work done!
Secondly, I'm working on a fungal species with very high levels of chromosomal polymorphism and large translocations (of Mbp), and I alr…