recipe nullarbor

Reads to report pipeline for bacterial isolate NGS data

Homepage

https://github.com/tseemann/nullarbor

License

GPL2

Recipe

/nullarbor/meta.yaml

package nullarbor

Versions

2.0.20191013-2,  2.0.20191013-1,  2.0.20191013-0,  2.0.20191007-0,  2.0.20191003-0,  2.0.20181010-5,  2.0.20181010-4,  2.0.20181010-2

Depends

• abricate >=0.9.8

• any2fasta >=0.4.2

• centrifuge >=1.0

• fasttree >=2.1.10

• iqtree >=1.6.12

• kraken >=1.1

• kraken2 >=2.0.7

• make >=4.2

• mash >=2.2

• megahit >=1.1.3

• mlst >=2.17.6

• newick_utils >=1.6

• perl >=5.16

• perl-file-spec

• perl-file-which

• perl-findbin

• perl-json

• perl-list-moreutils >=0.428

• perl-path-tiny

• perl-svg

• perl-text-csv

• perl-time-piece

• perl-yaml-tiny

• pigz

• prokka >=1.14

• quicktree >=2.5

• roary >=3.12

• samtools >=1.9

• seqtk >=1.3

• shovill >=1.0.9

• skesa >=2.3

• snippy >=4.4.3

• snp-dists >=0.6

• spades >=3.13

• trimmomatic >=0.39

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>)

Download stats

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/nullarbor/README.html)