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:

1.2.3-0,  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, 

1.2.3-0,  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 1.15.1.*

• biopython 1.79.*

• bwa 0.7.17.*

• clint 0.5.1.*

• htslib 1.15.1.*

• longshot 0.4.5.*

• medaka >=1.6.1

• minimap2 2.24.*

• multiqc 1.13.*

• muscle 3.8.*

• nanopolish 0.14.0.*

• pandas 1.4.4.*

• pip

• pyfaidx 0.6.0.*

• pysam

• pytest 7.1.3.*

• python 3.8.13.*

• pyvcf 0.6.8.*

• requests 2.28.*

• samtools 1.15.*

• tqdm 4.64.*

Required By:

Installation

With an activated Bioconda channel (see 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>)

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