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Posted here!
https://taylorreiter.github.io/2022-07-28-From-raw-metagenome-reads-to-phyloseq-taxonomy-table-using-sourmash-gather-and-sourmash-taxonomy/
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Hello!
I'm trying to use pyseer's elastic net feature to assess the effects of different variant groups on the phenotype, i.e. to find biologically plausible combinations of variants that predict t…
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Hello,
I have 40 bacterial MAGs that I used to create a tree with "gtdbtk classify_wf" option. Here is the command I used.
`gtdbtk classify_wf --genome_dir selected_genomes --extension fa --ou…
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Hello,
I have a problem with compilation of GPU-supporting `pp-sketchlib` under conda. By using this instruction: https://poppunk.readthedocs.io/en/latest/gpu.html
I end up with the following pack…
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Hi John,
As discussed, I've been running the --lineage-clustering option.
`poppunk --lineage-clustering --ref-db strain_db --external-clustering Global_TPA_SS14-mapped_2020-06-09.noINDELS.fix-m…
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Hi,
I am trying to run a kmer association study with PySeer 1.1.2 (installed with Conda). The kmers were generated using DSK then the combineKmers script from Seer. The distance matrix was generate…
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This happens with both example data and my own data.
Running it on Ubuntu 14.04.4 LTS
```
phenotypeseeker modeling dtoxin-phenotypeseeker.pheno
Compiled module "_likelihood_tree" not found. Wi…
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It has been requested by the community that the organisation of software in BioJulia should be made more modular than it currently is. Both for the benefit of both users and developers. We are reachin…