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**1. What were you trying to do?**
I want to test the new released `vg haplotypes` function.
**2. What did you want to happen?**
I want to do the haplotype sampling using HPRC MC graph and genera…
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PGGB exits are `smoothxg` with a non-zero status and does not continue to other modules.
```bash
module load pggb/0.5.3-Miniconda3
pggb -i 4Sim.fa -s 1000 -p 96 -n 4 -t 4 -S -m -o 4Sim_1K96 -V …
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Hi,
I have annotated a number of bacterial genomes with Prokka, which contain the respective genes in the gff files. However, after pangenome construction done with Panaroo at default threshold, the…
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**1. What were you trying to do?**
Inject a sam file into gam format. The sam file is the output of minimap2 mapping against the output of `vg paths -F` so the paths in the sam file ought to be e…
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Hello,
i was hoping if You can help me. I installed bactopia v3 and when I execute this command for 1 sample
bactopia --sample my-sample --R1 R1.fastq.gz --R2 R2.fastq.gz --outdir ime evrything g…
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Hi,
I am looking for your advice on building a pangenome graph among primates.
I am trying to build a primate pangenome using the macaque, gorilla, orangutan, chimp and human genomes (2x assemblie…
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Hi
I have attempted to execute a script using DeepVariant, and it has been running for approximately six days now without completion. I've only received intermediate outputs so far, without the exp…
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Hello,
I did pan-genome analysis with tormes before and I got the output. Now I reran the tormes with an updated date, however the **tormes_report.html** says: "Pangenome analysis was not performed."…
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**PLEASE DO NOT MAKE SUPPORT REQUESTS HERE**
Please the Biostars forum instead:
https://www.biostars.org/new/post/?tag_val=vg
I use GraphAligner to align "chr21 reads" to the "hprc-chr21.gfa"…
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Hi there,
I'm using minigraph-cactus to produce a pangenome from 6 haplotype-level phased assemblies. I used the command `cactus-pangenome ./js samplenames.txt --outDir atub_pg/ --outName atub_pg -…