recipe nullarbor

Pipeline to generate complete public health microbiology reports from sequenced isolates

Homepage

https://github.com/tseemann/nullarbor

License

GPL2

Recipe

/nullarbor/meta.yaml

package nullarbor

Versions

2.0.20181010-4, 2.0.20181010-2

Depends

• abricate >=0.8

• bwa >=0.7.17

• centrifuge >=1.0

• fasttree

• flash >=1.2

• iqtree >=1.6

• kraken >=1.1

• kraken2

• lighter >=1.1

• mash >=2.1

• megahit >=1.1

• mlst >=2.1

• newick_utils

• perl

• perl-file-spec

• perl-findbin

• perl-path-tiny

• perl-yaml-tiny

• pigz

• pilon >=1.22

• prokka >=1.12

• quicktree >=2.4

• roary >=3.0

• samclip >=0.2

• samtools >=1.8

• seqtk >=1.3

• shovill >=1.0

• skesa >=2.3

• snippy >=4.2

• snp-dists >=0.6

• spades >=3.6

• trimmomatic >=0.36

• velvet >=1.2.10

Required By

Installation

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

conda install nullarbor

and update with:

conda update nullarbor

or use the docker container:

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

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

Link to this page

Render an badge with the following MarkDown:

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