MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes, and Viruses) from metagenomic shotgun sequencing data with species-level resolution.

install guide:

Installation

Install the q2-metaphlan2 plugin of MetaPhlAn2 for QIIME2 with the following command:

conda install q2-metaphlan2 -c fasnicar -c bioconda

Testing installation

To test that the q2-metaphlan2 plugin is correctly installed you can follow these steps:

Download a sub-sampled (to 20k reads) skin metagenome from the HMP dataset:

wget https://bitbucket.org/biobakery/metaphlan2/downloads/SRS019033.fastq

Make the QIIME2 artifact:

echo -e "sample-id,absolute-filepath,direction\nSRS019033.fastq,$PWD/SRS019033.fastq,forward" > SRS019033.manifest
qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path SRS019033.manifest --output-path SRS019033.qza --input-format SingleEndFastqManifestPhred33

Run q2-metaphlan2:

qiime q2-metaphlan2 profile-single-fastq --i-raw-data SRS019033.qza --o-biom-table SRS019033_profile.biom --p-nproc 4 --verbose

Tutorial

You can find documentation and tutorials about MetaPhlAn2 in:

Help

If you experience problems when using MetaPhlAn2, please consider to report them on the MetaPhlAn2 Google Group (metaphlan-users@googlegroups.com).

Citation

Duy Tin Truong, Eric Franzosa, Timothy L Tickle, Matthias Scholz, George Weingart, Edoardo Pasolli, Adrian Tett, Curtis Huttenhower, and Nicola Segata MetaPhlAn2 for enhanced metagenomic taxonomic profiling Nature Methods 12, 902–903 (2015)