## What’s new in version 4 *
Adoption of the species-level genome bins system (SGBs,
http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html) * New MetaPhlAn
marker genes extracted identified from ~1M microbial genomes * Ability
to profile 21,978 known (kSGBs) and 4,992 unknown (uSGBs) microbial
species * Better representation of, not only the human gut microbiome
but also many other animal and ecological environments * Estimation of
metagenome composed by microbes not included in the database with
parameter --unclassified_estimation * Compatibility with
MetaPhlAn 3 databases with parameter --mpa3 ————-
Description
MetaPhlAn is a computational tool for profiling the composition of
microbial communities (Bacteria, Archaea and Eukaryotes) from
metagenomic shotgun sequencing data (i.e. not 16S) with species-level.
With StrainPhlAn, it is possible to perform accurate strain-level
microbial profiling. MetaPhlAn 4 relies on ~5.1M unique clade-specific
marker genes identified from ~1M microbial genomes (~236,600 references
and 771,500 metagenomic assembled genomes) spanning 26,970 species-level
genome bins (SGBs,
http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html), 4,992 of them
taxonomically unidentified at the species level (the latest marker
information file can be found here),
allowing:
- unambiguous taxonomic assignments;
- an accurate estimation of organismal relative abundance;
- SGB-level resolution for bacteria, archaea and eukaryotes;
- strain identification and tracking
- orders of magnitude speedups compared to existing methods.
- metagenomic strain-level population genomics
If you use MetaPhlAn, please cite:
Extending and improving metagenomic taxonomic profiling with
uncharacterized species with MetaPhlAn 4. Aitor Blanco-Miguez,
Francesco Beghini, Fabio Cumbo, Lauren J. McIver, Kelsey N. Thompson,
Moreno Zolfo, Paolo Manghi, Leonard Dubois, Kun D. Huang, Andrew Maltez
Thomas, Gianmarco Piccinno, Elisa Piperni, Michal Punčochář, Mireia
Valles-Colomer, Adrian Tett, Francesca Giordano, Richard Davies,
Jonathan Wolf, Sarah E. Berry, Tim D. Spector, Eric A. Franzosa, Edoardo
Pasolli, Francesco Asnicar, Curtis Huttenhower, Nicola Segata. Preprint
(2022)
If you use StrainPhlAn, please cite the MetaPhlAn paper and the
following StrainPhlAn paper:
Microbial
strain-level population structure and genetic diversity from
metagenomes. Duy Tin Truong, Adrian Tett, Edoardo
Pasolli, Curtis Huttenhower, & Nicola Segata. Genome Research
27:626-638 (2017)
In addition to the information on this page, you can refer to the
following additional resources.