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Thank you for creating such a great tool.
I have one question, your tool doesn't seem to generate the gene count matrix directly. If I want to generate a count table in addition to gene presence abs…
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## User story
>As a curator
>I want the post uploadscript to work as expected
>So that I can use it
## Acceptance criteria
>Given I have uploaded a dataset using the upload script
>Whe…
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Hi, iferres
Thank you for this software!
I am using simurg to test my pangenome software,
I wonder if can simurg result have paralogs, cause I found all gene ID forms as genomeX_geneX.
It …
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Dear Sam,
I'm using ggCaller v1.3.4, which I have installed using Conda (Docker is not available on the Linux cluster I'm using). I tested ggCaller with 10 Mtb genome assemblies I built using the c…
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Hi, me again,
There still appear to be issues with the pangenome reference generator. Lately, I wanted to build a core gene phylogeny using PhyloPhlAn with the core genes identified by Panaroo, but…
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Hi @gtonkinhill & @nzmacalasdair,
I am using `Panaroo v1.4.0` as part of a larger pipeline to make truth GFFs for 24 hybrid _E. coli_ assemblies to evaluate an AMR genotyping tool. I annotated my a…
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Issue: Case F0059468 (cust002) have a pathogenic variant in KRT6B that was not called in the WGS analysis. We found out that our patient's sister with the same disease was analyzed in another laborato…
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I have just installed Hybpiper2 and I am running through the tutorial data. It seemed to install fine, and check_dependencies finds all of the dependencies. However, the assemble stage fails at the ex…
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Hi,
I'm running the Panaroo with gff3 files without merging paralogs in strict mode.
panaroo \
--threads 20 \
--input {input} \
--out_dir {out_dir} \
…
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@dexink
- [x] SPBC660.17 - Schizosaccharomyces specific protein, uncharacterized
-> YGR016W (ER protein), from jackhmmr. Need t double check if more broadly conserved
- [x] (lcb3 removed)/ S…