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I am trying to index a gfa constructed from 3 closely-related melon sequences (to use with `vg map`) using `vg autoindex`. The gfa is ~2G, not particularly large or complex. I'm running the job on a m…
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Dear odgi team,
Thanks for developing `odgi`. I am working on a huge graph, so each processing step takes a long time. I was pruning some empty nodes from my graph to later explore it with some of…
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As visualization is not straightforward we strongly feel that it needs prototyping. Thus, we have decided to implement it as plugin for IGV.
We need to make some architectural decisions, so we need y…
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**Describe the bug**
NextDenovo/bin/nextgraph -a 3 -f 01.ctg_graph.input.seqs 03.ctg_graph/01.ctg_graph.input.ovls/seed_cns10.input.ovls -o seed_cns10.gfa
**Error message**
[INFO] 2022-11-10 10…
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Hi,
I successfully assembled an _A. thaliana_ genome for which I obtained two partially phased haplotypes of size 148.1 Mb (hap1) and 146.4 Mb (hap2), respectively. These files are in **.fasta** f…
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A GFA file ought to include both segments and gap records. It'd be preferable if gfakluge didn't segfault when encountering such a file.
```
H VN:Z:2.0
G * 6+ 50+ 121 58 FC:i:1
G * 6+ 225+ -57 5…
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**1. What were you trying to do?**
Get the read depth of alternative paths via `vg call`
**2. What did you want to happen?**
Read depth of alignments to be reported
**3. What actually happened…
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Hi,
on the Readme page, I have the impression that the output will contain two files, a GFF file "blocks_coords.gff" containing coordinates of the blocks, and file "alignment.maf" with the actual a…
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@lh3 In rGFA file (`test\MT.gfa`) there is a self loop, So can we expect graph generated with `minigraph -cxggs` or `minigraph --ggen` to contain self-loops or cycles?
gsc74 updated
2 years ago
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It'd be great if this and vg could speak in protobuf streams!