mhmism

Show relative abundance instead of n_obs

3

How can I show in the relative abundances for each taxa in the phylogenetic map instead of the number of observations (n_obs)?

Identify clusters of nodes

3

Hello, Thanks a lot for this wonderful mapper. I have been impressed by it so far. Is there a way to automatically identify clusters of closely connected nodes within the...

Abundance table

2

Hello, Thank you for this great pipeline! Is there a way to merge all groot reports into a single abundance table in a similar way to ASVs/OTUs tables? Thanks a...

How to determine relative abundances for RGI bwt for metagenomics?

2

Hello, I there a way to calculate relative abundances of the RGI bwt results for downstream samples comparison?

Hello, Thank you for this amazing tool and your continuous maintenance and support. I ran rgi bwt on some human shotgun metagenomics samples. I would like to know how to...

incorporate MetaPhlAn 4

2

I was wondering whether there are any plans for a major future update release (v4)?

Error running Genomad 1.7.1

2

Version 1.6.1 worked fine for me. After installing Genomad 1.7.1 (fresh install), I get the following error: Traceback (most recent call last): File "/gpfs/work5/0/gusr0570/conda/genomad_1.7.1/bin/genomad", line 6, in from genomad.cli import...

No rule to produce assembly

5

Hello, I would like to run Hecatomb only using the assembly or ctg_annotations module, but I end up with an error. Here is an example code: hecatomb run --reads /reads...

Filtering out host (human) genome beforehand?

3

Thank you for this wonderful tool! Should we filter out the host (human) genome before executing the pipeline e.g. using kneadData or fastp? the same also applies to the PhiX...