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setup_metaphlan.sh uses "module load python/3.8" to access a sufficient python install (3.8) for the venv for metaphlan. This is at least one example of a feature (module or "lmod") that could be repl…
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Hello,
I just installed hclust2 from tagged release 1.0.0, in order to be abble to generate heatmaps form metaphlan outputs.
in order to test it I ran the test as described here: https://github…
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Dear curatedMetagenomicData Maintainers,
Considering that GTDB taxonomy is a cornerstone for microbial genomics research, I was wondering if there is a possibility to also provide GTDB taxonomy lab…
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Dear luis,
Since also metaphlan 3 is out, maybe you can add this as well?
https://huttenhower.sph.harvard.edu/metaphlan/
Cheers,
Ulrike
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See: https://github.com/spdx/license-list-XML/issues/2294
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Very exciting work!
I want to give it a go with my own marker genes database.
The publication states 'SameStr can be easily adapted for use with [...] alternative, user-provided, marker sequences.'
…
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I have read a couple of comparisons that found that Kraken is performing a lot worse than mOTUs2 and MetaPhlAn 3.
![image](https://user-images.githubusercontent.com/631218/113280302-d28af480-932f-1…
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@lkalmar can you list here on this issue all the software that is used in the course?
So we can keep track of things for future iterations of the course.
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[BioBakery](https://huttenhower.sph.harvard.edu/tools/) Modules:
- Taxonomic profiling using [MetaPhlAn 3.0](https://github.com/biobakery/metaphlan)
- Functional profiling using [HUMAnN 3.0](htt…
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### Description of the bug
Hello everyone,
I am getting the following error during the taxpasta standardise function using the data from the tutorial age:
```
Execution cancelled -- Finishing …