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

1.2.2-0,  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 0.23.0.*

• pip

• pysam 0.16.0.1.*

• pytest

• python 3.6.13.*

• 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>)

Download stats

Link to this page

Render an badge with the following MarkDown:

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