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As suggested by @heuermh during the BOSC 2021 CoFest - thank you!
- rGFA https://github.com/lh3/gfatools/blob/master/doc/rGFA.md#the-reference-gfa-rgfa-format
- GFA 1.0 http://gfa-spec.github.io/G…
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Hi,
I am running the step-by-step pangenome pipeline and failed at `filter_paf_deletions` in `cactus-graphmap`
Based on this log `Exit reason: MEMLIMIT`, it should be caused by insufficient memo…
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Hi there,
Is it possible to merge pangenome graphs from independent runs? I know panaroo has that option, and would like to know if it would be possible to do so with ppanggolin.
If not, could you…
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First off, the only way I have found that actually works to incorporate custom data is to explicitly add records to config.json and recompile the app: no "custom data (mounted files)" appears as an op…
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The abundance of a hash in a pangenome sketch is the amount of genomes that contain that hash per lineage.
When we get to creating the rank table, these sketches may be merged. The pangenome element…
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Hello! I get the result of pangenome. but I don't know the meaning of the file. like pan-genome.wga.conensus.stats,pan-genome.wga.core.stats, pan-genome.wga.newseq.stats and files in tmp. like An-1.co…
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Thanks for writing `taxor` and including useful databases!
What the community (or maybe just me) really wants is a database that covers more of the microbial kingdom, but with the benefit of GTDB f…
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Hi,
After running the `cactus-graphmap-split`, I found a few samples can have very large `_AMBIGUOUS_` contig. I manually checked some samples and found it is due to a large contig that mapped to 2…
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- PPanGGOLIN v2.0.5
Hi, after running and creating the pangenome file with this command, for about ~1600 GFFs:
```sh
ppanggolin \
workflow \
--cpu 24 \
--anno ppanggolin_samplesh…