recipe artic

ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore

Homepage

https://github.com/artic-network/fieldbioinformatics

License

MIT

Recipe

/artic/meta.yaml

package artic

Versions

1.2.1-0,  1.2.0-0,  1.1.3-1,  1.1.3-0,  1.1.2-0,  1.1.1-1,  1.1.1-0,  1.1.0_rc2-0

Depends

• artic-porechop 0.3.2pre.*

• artic-tools 0.2.6.*

• bcftools 1.10.2.*

• biopython >=1.76

• bwa 0.7.17.*

• clint

• htslib 1.10.2.*

• longshot >=0.4.1

• medaka >=1.0.3

• minimap2 2.17.*

• multiqc

• muscle >=3.8

• nanopolish >=0.13.2

• pandas <1

• pip

• pysam >=0.15.3

• pysam >=0.16.0.1

• pytest

• python >=3

• pyvcf >=0.6.8

• requests

• samtools 1.10.*

• tqdm

Required By

Installation

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

conda install artic

and update with:

conda update artic

or use the docker container:

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

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

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/artic/README.html)