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?
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)
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
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.
Great! I will get the new version today and test it.
Sorry to bother, do you know the default value of min_ab option in metaphlan?
min_ab is set at 0.1 but it is used only for the
clade_specific_strain_tracker analysis type