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Hi Giorgio,
Thanks for the great library!
I came across an issue when using `merge_linear_paths` with `enable_tracking=True`. Not sure if it's a general problem or maybe a version incompatibility? T…
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After #1371 (compact De Bruijn graph work) and #1372 etc. (assembly), can we now input/output [FASTG](http://fastg.sourceforge.net/) or [GFA](https://lh3.github.io/2014/07/19/a-proposal-of-the-grapica…
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Interest have been expressed about visualizing graphs from pggb into Panache ( cf nf-core/pangenome#197), but the steps to convert formats are currently unclear.
Some documentation highlighting how…
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I am trying to generate indexes for giraffe of a GFA file generated using PGGB but I am getting the following error continuously.
Command used : vg autoindex -w giraffe --prefix pggb_real --gfa p…
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Hi there,
I'd be interested in mapping noisy long-reads to assembly graphs (in GFA format), to untangle paths through repetitive parts of the graphs.
Here is another github issue (https://github…
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The FASTQ parsing is currently tightly coupled with spades output. Simple nodes with no intra-sequence branching fail to load. It appears this is due to shapes-specific parsing of node names and expli…
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@benedictpaten wants Giraffe to be "fully simple". This has two elements, as I understand it:
* We should have standards and specs for input formats we want from HPRC, to run on
* We should have a p…
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**1. What were you trying to do?**
I would like to convert gfa file into vg format.
**2. What did you want to happen?**
killed or Terminated.
**3. What actually hap…
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Hello,
I wish to test astarix on small test data available in [minigraph repository](https://github.com/lh3/minigraph/tree/master/test). The graph is in GFA format with zero overlaps.
For this, …
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Now that `vg convert` lets us go direct from GFA to handlegraph models, we should be able to work fully with those models.
Some tools default to producing .vg files. We need to pick a good default …