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Schematize should be running as a component inside of JBrowse2. This is a separate repository at https://github.com/graph-genome/jbrowse-components which should check out Schematize repo as a submodu…
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We need to document all necessary steps to go from https://github.com/vgteam/odgi over https://github.com/graph-genome/component_segmentation to https://github.com/graph-genome/Schematize/ and visuali…
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In https://github.com/ekg/freebayes/issues/419 @tseemann [asked if vg was ready for bacterial pangenomics](https://github.com/ekg/freebayes/issues/419#issuecomment-377646948). My response better fits …
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Hi!
I want to reconstruct a HPRC graph with HG002, and using the command `cactus-pangenome ./js-grch38 ./hprc-v1.1-mc.seqfile --outName hprc-v1.1-mc-grch38 --outDir hprc-v1.1-mc-grch38 --reference GR…
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@dentearl , @thiagogenez , @diekhans, @epaull and @benedictpaten,
I'm trying to build pangenome graph with MHC genomes from [Zenodo](https://zenodo.org/record/6617246#.ZC0OQ-xBxhE)
Command used …
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@lh3, I'm curious to know , whether we can convert `GFA` to `rGFA`? . As per [rGFA](https://github.com/lh3/gfatools/blob/master/doc/rGFA.md) format, we need to maintain 3 additional information along…
gsc74 updated
1 month ago
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@cmarkello has some graphs that have taken over 9 days to GCSA index and are still going.
They were built with the GRCh37 1000 Genomes data, and he's using the GBWT haplotypes to prune the graph befo…
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Is strobealign a good basis for the following application:
We would align against a pangenome FASTA. So we might have 100 genomes in this system. Downstream we project the alignments into a graph f…
ekg updated
10 months ago
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Hi
I'm currently trying to load in a BED or GFF file when loading in the GFA. No gene coordinates are overlayed.
I've tried with a BED file and GFF:
GFF:
```
Morex_v3_chr6H pgsb gene 516806…
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Hi!
Thank you for developing such a great software!When I run Minigraph-Cactus, there are no errors in the first three steps, but when I run cactus-graphmap-join to get the pangenome graph, the follo…