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## The need
This feature would add UI elements to the inspect page for the user to manually enter start/stop coordinates based on position within the parent contig and retrieve subsequent sequence …
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I'm having trouble using the provided GFF3 annotations from https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13.draft_v1.1.gene_annotation.v4.gff3.gz
Here's w…
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Back at MemPan23, we heard the following refrain a few times:
> Pangenomics is one of those fields that have been "solved" by the discovery of the right data structure. That data structure is the GFA…
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**1. What were you trying to do?**
I was attempting to use `vg autoindex` to create a graph using T2T-CHM13 as a reference and a VCF file built from 1KGP variants mapped to said reference.
*…
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This is not really a software issue, but a general question about the paraphrase algorithm. If it is aligning reads to one member of the gene family, how can it distinguish if a read is from a gene or…
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Hi @AndreaGuarracino,
I was trying to extract `grch38#chr1:13104252-13122521` from the Chr1 HPRC pangenome graph. However, I ran into lot's of trials and errors until I somehow got what I wanted. S…
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Hi,
I have built the Graph Pan-genome, how should I use the tool to characterize it and dig deeper into the potential information it contains. Or is there any other analysis tool recommended.
Best…
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## Short description of the problem
Can't visualise the pangenome with average nucleotide identity, even when ANI is imported.
## anvi'o version
Keep the header of this section, but replace …
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Right now, vg is a strong reference implementation of basic ideas in graphical pangenomics, but its performance suffers in a number of contexts due to a number of design decisions that are hard to unw…
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Hi,I got the following error with the command(_**odgi extract -i GRAPH -b BED -o - -c 0 -d 10 --full-range -t 30 -P**_ ), how should I fix it?
Besides, how can I keep more additional inf…