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Published August 22, 2022 | Version 4.beta.3
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biobakery/MetaPhlAn: 4.beta.3

Description

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. What was changed in version 4:

  • Adoption of the species-level genome bins system (SGBs).
  • 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

Files

biobakery/MetaPhlAn-4.beta.3.zip

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Additional details

Related works

Is supplement to
https://github.com/biobakery/MetaPhlAn/tree/4.beta.3 (URL)