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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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Large genome / metagenome could generate very huge assembly graph. We need to see how to load them properly.
Few ideas straight from the head:
* Switch to GFA parser from https://github.com/lh3/…
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I'd like to use adaptive banded global alignment (with affine gaps) instead of edlib. Switching between the different algorithms should be possible.
The best target for this is @ocxtal's https://gi…
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Hi vgteam!
I am trying to understand how `vg` handles different phenotypes of a diploid organism like `1|0`and `1|2` (phased) or `1/0`and `1/2` (unphased). Therefore I took a look at your tiniest …
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Dear Heng,
I am trying to build a rgfa from two large genomes (>10Gb). They are both finished down to chromosomes. I get the following output:
```
[M::main::23.960*1.00] loaded the graph from "…
fbemm updated
4 years ago
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Dear VG Team Members,
I hope this message finds you well.
While using the vg giraffe tool to align short reads, I encountered an issue similar to the one described in issue #4171 . Specifically,…
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I'd like to be able to do a conversion of a GAM output to BAM without realignment against the surjected path. I have a little script that converts regions of a GAM file to a coverage based view (attac…
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* Model around GAF format: list all paths, some paths queries (like in #4)
* Maybe join with BLAST hits and their paths
@ekg I started to draft better UI for paths. Unfortunately, I cannot che…
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For: Kaytie Innamorati @innamoratika
**Goal:** We want to show related individuals and blocks of individuals for viral sequences. We should be equivalent or harness information on nextstrain.org. …
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I am trying to run the following command using version 2.6.2
cactus-minigraph jobstore test_seqfile.txt first_run.gfa --workDir /workdir --reference WN.1 --binariesMode local --defaultCores 4
I …