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Hi, How to add new sample genomes and contigs to an existing pan-genome producted by PGGB, and whether it can be done directly using the Minigraph or GraphAligner tool. Any suggestions on how to do th…
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When extracting a subgraph using a BED file via `-b` the resulting subgraph contains all BED range(s) specified plus all nodes between these ranges which are not touched by any path!
It would be nic…
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We received the simulated reads from the authors. However, it is not clear how to
a) extract Mapping Quality of the alignments,
b) derive the equivalent reference position of the reads that we…
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Hello! Sorry I'm bothering you again.
The genome size of this species is around 12M and I have partitioned it chromosomeally in advance. The following command ran fast in 34 samples.
`for i in 1 …
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Dear eblerjana,
I have a question regarding the following: In the graph pangenome constructed for the species I am studying, there are some large SV segments. Within these particularly large SV seg…
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https://github.com/rmcolq/pandora/blob/565c1572f2c535db20c45062d359055d04a7659a/src/localPRG.cpp#L1406-L1407
I've triggered this error and don't really know why/how? Any suggestions on how to get t…
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Hi
I'm getting an error with one of my graphs. I'm trying to build from GFA and am getting the following error:
```
odgi build -t 32 -P -g barley_pangenome_graph_2H.gfa -o barley_pangenome_grap…
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**1. What were you trying to do?**
I have been using FSA to align about 20 de-novo-assembled genomes that are about 1MB long. They are from different individuals in the same species. FSA runs, but …
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Matthew:
Thanks as always!
I think it useful to have the discussion in the Google group (I find I use it quite a lot). So I will follow up here and submit a bug report.
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Version = si…
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I'd like to extract reads from a .gam file that do not align to any nodes that are in a reference path. My end goal is to identify coverage and depth of likely insertions.
Commands that strike me a…