recipe singlem

SingleM is a tool to find the abundances of discrete operational taxonomic units (OTUs) directly from shotgun metagenome data, without heavy reliance on reference sequence databases. It is able to differentiate closely related species even if those species are from lineages new to science.

Homepage

https://github.com/wwood/singlem

License

GPL3 / GNU General Public v3 (GPLv3)

Recipe

/singlem/meta.yaml

package singlem

Versions

0.13.2-0

Depends

• biom-format >=2.1.6

• biopython >=1.64

• dendropy >=0.4.0

• diamond >=0.9

• expressbetadiversity

• extern >=0.0.4

• graftm >=0.12.2

• h5py

• hmmer >=3.1b1

• krona >=2.4

• matplotlib-base >=2.0.2

• mfqe >=0.5.0

• orator >=0.9.7

• orfm >=0.2.0

• pandas

• pplacer >=1.1.alpha17

• python >=3.6

• smafa >=0.5.0

• squarify >=0.3.0

• tempdir >=0.6

• vsearch

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install singlem

and update with:

conda update singlem

or use the docker container:

docker pull quay.io/biocontainers/singlem:<tag>

(see singlem/tags for valid values for <tag>)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/singlem/README.html)