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hello all,
thanks a lot for the wonderful package,
I'm trying to use loadFromMetaphlan to create a TreeSummarizedExperiment with Metaphlan 4 output.
"file_path
Error: 'file' must be a singl…
J5886 updated
4 months ago
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**Name the workflow**
Taxonomic-Profiling-Minimap-Megan and Taxonomic-Profiling-Diamond-Megan
**Describe the question and context**
Is it possible to add internal sequences to the taxonomy databa…
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**Hello, I would like to ask**
Is there any **difference** in algorithm between this and Pathoscope, and is it **more accurate** in identifying pathogenic microorganisms? Is there an advantag…
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Hi,
I've been trying to run the sylph sketch command on a forward and reverse short read set using command:
`sylph sketch -1 4914_4_cat_R*`
The reads files are in form of:
`4914_4_cat_R1.…
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Hi,
Thanks for the developing of the taxonomic profiling tool.
in my case, the mitag download failed several times. Are there other ways to complete this step?
Looking forward for your reply.
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`extract_genus` needs to speed up.
- One option is preprocess the parquets before saving. (Not ideal, because stable vs current resources are then different)
Relevant SO post: https://stackoverflow…
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## Short description of the problem
I end up with different results per sample when I run co-assembly on all my samples at once vs going through the anvio pipeline for subsets of my files.
## an…
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Name the workflow
Taxonomic-Profiling-Minimap-Megan
Describe the question and context
When creating the index file for the `minimap2` workflow, the resulting `.mmi` exceeds the expected size by a…
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(Part of review thread https://github.com/openjournals/joss-reviews/issues/6062)
Overall, the paper reads well, and I am convinced of your pipeline's value both in terms of
need for the community…
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**Describe the bug:**
When trying to perform pathway profiling I can't complete it because the number of genomes in taxonomy does not match the number of genomes in "identifier_mapping". On further r…