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Thank you very much for providing such a useful tool!
I successfully used it to assemble the genome of a diploid orchid. I want to get the gfa file of the diploid assembly, similar to the hifiasm_r…
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Hi,
last year I ran the below pipeline. In the meantime, minimap2 came out, racon supports FASTA files now and racon_wrapper.py has been developed.
For my new dataset, I have only FASTA files and…
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Hello,
I am trying to use a variation genome graph to genotype SVs on more samples sequenced with short-reads, and I'm trying different avenues (see 1)graph from vcf + giraffe and 2) graph with pggb+…
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Hi there,
I have new pacbio long-reads assembled into a 2.2G genome. I want to use racon to do polishing. When I run racon1.3.1 using following command
`racon -t 34 LT2.merged.filt2k.fasta LT2.2…
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I try to convert a gfa input into a vg graph and run into a segmentation fault.
`/ebio/abt6_projects9/abt6_software/bin/vg/bin/vg view -v -F TwoPaCo/twopaco_TAIR10_masked_9.gfa > TwoPaCo/twopaco_TA…
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From @crockosi:
> Expid 66266 tile 80061 from tonight 202012006 has two guide stars that have close friends in the postage stamps.
Check if the GFA_TARGETS isolation cuts are still being applied…
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Often, multiple contigs in the reference fasta will belong to the same construct (such as a viral vector or plasmid). It would be nice if there were a way to describe the ordering of the component con…
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Hi
I'm trying to load my GFA file, but I'm getting an error.
```
gfaestus *.smooth.gfa *.smooth.chop.og.lay
loading GFA
loading GFA with 734 nodes, 1003 edges
adding nodes
adding edges
add…
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I just encountered this. My GFF files only contain the feature type "gene." I wrote out the GFF files myself but they are correctly formatted according to gff3validator. I am able to run the test data…
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1. What you were trying to do
getting the graph in GFA format with vg view on the "tiny" example with simple tiny.vcf files from your test directory
2. What you wanted to happen
see above
…