Metaxa2

Metaxa2: Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data
Johan Bengtsson-Palme, Martin Hartmann, K. Martin Eriksson, Chandan Pal,
Kaisa Thorell, D.G. Joakim Larsson, R. Henrik Nilsson
Molecular Ecology Resources (2015). doi: 10.1111/1755-0998.12399

Download the Metaxa2 package (version 2.2.3)

Read the Metaxa2 manual

Read the FAQ

Looking for the previous version of Metaxa? It is still available, here.

Please e-mail me if you encounter bugs or have questions, but first check out the FAQ! If you do not find your answer there, then feel free to e-mail me. My e-mail address is firstname.lastname[a]microbiology.se (and my name is Johan Bengtsson-Palme).

Version history

  • 21st January 2013 – 2.0 beta – first public release.
  • 4th March 2013 – 2.0 beta 2 – support for blast+ and paired-end reads in FASTA format.
  • 9th April 2013 – 2.0 beta 3 – LSU support, rewritten classifier with improved taxonomic prediction.
  • 22nd July 2013 – 2.0 beta 4 – cleaner database with less bad sequences, HMMER 3.1 compatibility, 12S
    support reintroduced.
  • 10th November 2013 – 2.0 beta 5 – taxonomic classifier much improved, minor bug fixes.
  • 26th November 2013 – 2.0 release candidate – software taken out of beta.
  • 28th January 2014 – 2.0 release candidate 3 – cosmetic fixes.
  • 5th November 2014 – 2.0.1 – stable release with slightly improved classifier.
  • 7th April 2015 – 2.0.2 – slight improvements to the classifier, minor bug fixes.
  • 2nd October 2015 – 2.1 – introduced Metaxa2 Diversity Tools, added the genome and reference modes, minor bug fixes.
  • 9th October 2015 – 2.1.1 – fixed a bug in metaxa2_uc.
  • 15th January 2016 – 2.1.2 – enhanced memory efficiency.
  • 7th April 2016 – 2.1.3 – features added to the metaxa2_uc and metaxa2_rf tools.
  • 14th December 2017 – 2.2 beta 8 – added support for custom databases and improved the classifier (public beta).
  • 1st January 2018 – 2.2 beta 9 – added support for custom databases and improved the classifier (public beta).
  • 28th January 2018 – 2.2 beta 10 – added support for VSEARCH (public beta).
  • 15th June 2018 – 2.2 – stable version including the Metaxa2 Database Builder
  • 15th June 2020 – 2.2.1 – updated compatibility with HMMER 3.3
  • 14th August 2020 – 2.2.2 – bug fixes related to the database repository
  • 13th February 2021 – 2.2.3 – fixed a genome mode file reading bug

If you for any reason would be interested in an older version of Metaxa or Metaxa2, please e-mail me at the address below.

If you use Metaxa2 in your research, please cite it as:

Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2: Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data. Molecular Ecology Resources (2015). doi: 10.1111/1755-0998.12399

If you use the Metaxa2 database builder, please cite it as:

Bengtsson-Palme J, Richardson RT, Meola M, Wurzbacher C, Tremblay ED, Thorell K, Kanger K, Eriksson KM, Bilodeau GJ, Johnson RM, Hartmann M, Nilsson RH: Metaxa2 Database Builder: Enabling taxonomic identification from metagenomic and metabarcoding data using any genetic marker. Bioinformatics (2018). doi: 10.1093/bioinformatics/bty482

Contact information

Johan Bengtsson-Palme (firstname.lastname [at] microbiology.se)
University of Gothenburg
Department of Infectious Diseases
Guldhedsgatan 10
413 46 Göteborg

6 Comments
  1. Mikkel Winther Pedersen

    Hi Johan,

    Very interesting pipeline Metaxa 2.0, I have been testing it out on a metagenomic dataset of mine. I have a question related to the database imbedded in the programme. Would it be possible to use a database containing other taxonomically distinct genes? By referring to an external database, and what about the HMMs’s could these be substituted too?

    All the best,
    Mikkel

  2. Johan

    Dear Mikkel,

    I am not 100% sure what exactly you mean by “other taxonomically distinct genes”. Do you refer to, e.g., the rpoB genes or some other genetic barcode? Indeed this is somewhat like what we have done with ITSx, but it turned out to be a much larger task than we envisioned. That said, Metaxa2 is in principle designed to deal with other genes as well, but that would require some changes to the code. Better ease-of-use for custom databases could be a suggestion for upcoming updates to the program, given that it is something that users need. Please send me an e-mail if you want to discuss this option further!

    Best,
    Johan

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