Skip to content

Commit

Permalink
Updates README
Browse files Browse the repository at this point in the history
  • Loading branch information
abmiguez committed Aug 23, 2022
1 parent e112ad4 commit 6d62358
Showing 1 changed file with 13 additions and 1 deletion.
14 changes: 13 additions & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -22,12 +22,24 @@ MetaPhlAn 4 relies on ~5.1M unique clade-specific marker genes identified from ~

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)
[**Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4.**](https://doi.org/10.1101/2022.08.22.504593) 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.**](http://genome.cshlp.org/content/27/4/626.full.pdf) *Duy Tin Truong, Adrian Tett, Edoardo Pasolli, Curtis Huttenhower, & Nicola Segata*. Genome Research 27:626-638 (2017)

-------------

## Installation
The best way to install MetaPhlAn is through conda via the Bioconda channel. If you have not configured you Anaconda installation in order to fetch packages from Bioconda, **please follow [these steps](https://bioconda.github.io/user/install.html#set-up-channels) in order to setup the channels.**

You can install MetaPhlAn by running

```
$ conda install -c bioconda python=3.7 metaphlan
```

For installing it from the source code and for further installation instructions, please see the Wiki at the [Installation](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#installation) paragraph.

-------------

Expand Down

0 comments on commit 6d62358

Please sign in to comment.