- recipe metagenome-atlas
ATLAS - Three commands to start analysing your metagenome data
- Homepage:
- Documentation:
- Developer docs:
- License:
BSD / BSD-3-Clause
- Recipe:
- 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
numpy
1.21.*
pandas
>=1.2,<1.5
pyarrow
>=8
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¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/metagenome-atlas/README.html)