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**1. What were you trying to do?**
I am trying to build an index
****2. What did you want to happen?****
vg autoindex --workflow giraffe -g graph_genome.gfa -p PN -t 8
**3. What actually hap…
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I have a similar but perhaps different issue to Issue #45 (No sequences in gfa - unable to convert to fasta). I have used the `-f` option (`miniasm -f reads.fq overlaps.paf`) but there are no sequen…
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I'm interested in using splice graphs as reference systems in vg. It would be possible to use ChopStitch's output to do so directly if it were able to write [GFA](https://github.com/GFA-spec/GFA-spec)…
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Hello, I have successfully completed the assembly, but now I want to evaluate the quality of the genome assembly. The software I want to use at present is Busco. But how do I convert this GFA format f…
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Dear developer!
I have a dozen high-quality genomes of diploid mammals, and I have obtained a graphical pan-genome through Minigraph-Cactus, which we think is accurate and perfect. Of course, we want…
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Hello,
I want to generate the pcf file but I get the following error when running the vcf2xg.sh in my own data. The vcf file was generated using minigraph-cactus pangenome pipeline.
./vcf2gfa/v…
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Hi,
I want to map short reads to a large gfa graph and get the reads information about which paths mapped to and which postion (nodes id) in the paths. The big gfa graph merges the gfa graphs from…
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Today I was trying to extract threads from a GBWT as paths. I had to pull them out as GAM and augment the graph with them, using many gigabytes of RAM for a single gene (p53) and 5000 haplotypes.
I…
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Hello!
I am using seqwish for pan-genome construction, and I have a question about the alignment result.
Typically, according to the pggb pipeline, the wfmash tool is used for mapping and the re…
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I'm trying to get GFA output from a .vg file made by vg chunk.
It's not possible due to memory exhaustion (I'm on a puny system).
I can convert to PackedGraph format with vg convert:
```
vg …