recipe metagenome-atlas

ATLAS - Three commands to start analysing your metagenome data

Homepage:

https://github.com/metagenome-atlas

Documentation:

https://metagenome-atlas.rtfd.io

Developer docs:

https://github.com/metagenome-atlas/atlas

License:

BSD / BSD-3-Clause

Recipe:

/metagenome-atlas/meta.yaml

Links:

doi: 10.1101/737528

Atlas is a easy to use metagenomic pipeline # Quick Start

Three commands to start analysing your metagenome data: ```

mamba install -c bioconda -c conda-forge metagenome-atlas atlas init --db-dir databases path/to/fastq/files atlas run

``` All databases and dependencies are installed on the fly in the directory `db-dir`. You want to run these three commands on the example_data on the GitHub repo. If you have more time, then we recommend you configure atlas according to your needs.

- check the `samples.tsv` - edit the `config.yaml` - run atlas on any cluster system

For more details see documentation.

package metagenome-atlas

Versions:

2.14.0-0,  2.13.1-0,  2.13.0-0,  2.12.0-1,  2.12.0-0,  2.11.1-0,  2.11.0-1,  2.11.0-0,  2.10.0-0, 

2.14.0-0,  2.13.1-0,  2.13.0-0,  2.12.0-1,  2.12.0-0,  2.11.1-0,  2.11.0-1,  2.11.0-0,  2.10.0-0,  2.9.1-0,  2.9.0-0,  2.8.2-0,  2.8.1-0,  2.8.0-0,  2.7.0-0,  2.6a4-0,  2.6a2-0,  2.6a1-0,  2.5.0-0,  2.4.5-0,  2.4.4-0,  2.4.3-0,  2.4.2-0,  2.4.1-0,  2.4-0,  2.3.5-0,  2.3.4-0,  2.3.3-0,  2.3.2-0,  2.3.beta2-0,  2.2.0-0,  2.1.4-1,  2.1.4-0,  2.1.3-0,  2.1.1-0,  2.0.6-1,  2.0.5-1,  2.0.4-1,  2.0.3-1,  2.0.1-1,  2.0.1-0

Depends:

• bbmap >=39.01,<40

• click >=7

• cookiecutter

• graphviz

• mamba

• networkx

• numpy 1.21.*

• pandas >=1.2,<1.5

• pathlib

• pyarrow >=8

• pygments

• python >=3.8,<3.11

• ruamel.yaml >=0.17

• snakemake-minimal >=7.18.1,<7.19

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install metagenome-atlas

and update with:

conda update metagenome-atlas

or use the docker container:

docker pull quay.io/biocontainers/metagenome-atlas:<tag>

(see metagenome-atlas/tags for valid values for <tag>)

Download stats

Link to this page

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