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Hi, I am running CAT to annotate contigs from metagenomes that are known to be E. coli by several other approaches. For example, greater than 99% average nucleotide identity with reference E. coli ge…
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I want to investigate HGT among an eukaryote and two of its symbiont bacteria (all pairs:: EK-bacteria1, EK-bacteria2, bacteria1-bacteria2). Is it possible to use your pipeline for this purpose?
Th…
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Related to #228, opening a new bug since I can't reopen the old one and this is a new example.
We are still seeing failures in gapfilling for Archaea with version 1.3.1. I attached an example from…
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Hi,
I am trying to use the function taxa.compare.
I got a data.frame with 2 factors : chimio : Pre, Post and the number of the patients.
Here the structure of the data.frame df:
chimi…
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How would it be possible to have a summary made out of a chunk? With a prompt named: `summary_gen.yaml`
**_EDIT: While I had trouble getting my head around the code in `./original`, I started from …
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In `create-genome-phylogeny` no list for "all". RAXML also errors with options
```
# different ribosomal markers for archaea/bacteria/all
bacteria_list = ['rpL14_bact','rpL15_bact','rpL16_bact',…
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Dear Chen,
I hope this message finds you well.
I have encountered an issue while using the `mStat_generate_report_long()` function from the MicrobiomeStat package. Below is the script I am using…
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Came up during discussion with @fedarko
Might be useful to allow the user to specify a regular expression for which to search the feature space. This should hopefully allow users to specify (almos…
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Hi:)
I ran kraken2.1.2 for my mice gut microbiome shotgun metagenomic analysis. I built a custom db by using the following command
```
kraken2-build --download-taxonomy --db refseq
kraken2-build …
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After installing the `quast` package, the recipe say to manually download the BUSCO databases, via `quast-download-busco`. This program fails with:
```
Downloading BUSCO database...
Downloading …