MetaPhlan output

Microbial community profiling MetaPhlAn
1

Hi,

First, thanks for the pipelines!
I use Metaphlan3 with the tax_level “g” parameters and I have duplicates (some genus are present 4 times) in my output. I wonder if it is normal?

I also wonder if there is a way to adapt Metaphlan and Humann output to phyloseq by any chance?

Cheers,

Nico

2

That’s weird, could you share with me the bowtie2out file and the command line you used?

About importing MetaPhlAn and HUMAnN profiles, have a look at this function here https://gist.github.com/lwaldron/512d1925a8102e921f05c5b25de7ec94 , the newick file for MetaPhlAn 3 can be found in the GitHub repository (https://github.com/biobakery/MetaPhlAn/blob/master/metaphlan/utils/mpa_v30_CHOCOPhlAn_201901_species_tree.nwk)

3

Hi!

Thanks for the tree and the link.

Sure, here is an example of the bowtie2out and the command used was:

for sample in $(cat Sample_ID);do metaphlan $sample.PE.fasta.bowtie2out.txt --nproc 10 --input_type bowtie2out --tax_lev “g” -o $sample.profiled_counts_metagenome_genus.txt; done

Cheers,

Nico

7-H0.PE.fasta.bowtie2out.txt
9-H2.PE.fasta.bowtie2out.txt
merged_genus_abundance_table.txt

4

Hi Nico,
The presence of duplicate genera was due to a bug present in merge_metaphlan_tables, I fixed that, you can get the fixed script on the GitHub repository, I’ll push a new build on conda soon.

5

Hi!

Great! I will get the new version today and test it.

Cheers

6

Hi again!,

Sorry to bother, do you know the default value of min_ab option in metaphlan?

Cheers

7

min_ab is set at 0.1 but it is used only for the clade_specific_strain_tracker analysis type