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There's not a lot of standalone tools for bubble popping, so thanks for implementing this one. It's an interesting problem, and I'm a big fan of standalone implementations of core assembly algorithms.…
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Hi, I tried to use GraphAligner(GraphAligner -g CPC.HPRC.Phase1.CHM13v2_Non-W.gfa -f /HJ.stLFR_CCS.maternal.fasta.gz -a aln.gam -x vg), But I got several errors message.Can you give me some suggestion…
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**Describe the bug**
In the output of `vcfwave`, the phased genotypes are not consistent with the input VCF.
**To Reproduce**
Here are some examples of the incorrect phased genotypes.
Inpu…
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I've been recording some of this information in #384 but it seemed like a good idea to have a dedicated issue.
**Goal**: dom set differential abundance
**Need**: tractable catlas (# domsets ~= # g…
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Hi there,
Thanks for this great tool. I noticed that, in both the HPRC reference release paper and the original paper describing this tool, you employ complex pre and post pangenie variant filterin…
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For the 1001 Genomes project we have 23 *A. thaliana* genomes that are 150 Mbp. Each genome will have its own annotation of >30,000 genes for a total of 750,000 paths. This requires some consideratio…
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Hi,
First, congratulations on the development of Anchorwave, it seems a great addition to the Comparative Genomics toolkit!
I have several questions, the majority linked to the "Empty CDS file f…
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Hello,
A while back I aligned simulated reads to a graph using vg v1.4.0-1017-g0042f59. As part of a new test, I've reindexed the graph and remapped the simulated reads using v1.4.0-2142-gfe5e050 (…
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Hi,
I am running smoothxg on GFA graphs produced via vg construct > vg view.
```
cgroza@blg9122:~/.../sv-graph/graphs $ ~/smoothxg/bin/smoothxg -g chr1.vg.gfa
terminate called after throwing an in…
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Hi Jonas A:
I have tried to construct and index spliced pangenome graph using the this gtf,but an error has occurred. I tried to solve the problem but the result was not satisfactory. So, can yo…