recipe snippy

Rapid bacterial SNP calling and core genome alignments

Homepage

https://github.com/tseemann/snippy

License

GPL / GPL-2.0

Recipe

/snippy/meta.yaml

Links

biotools: snippy

package snippy

(downloads) docker_snippy

Versions

4.4.0-0, 4.3.6-0, 4.3.5-0, 4.3.3-0, 4.2.3-0, 4.1.0-0, 4.0.7-0, 4.0.5-0, 4.0.2-0, 3.2-1, 3.1-4, 3.1-3, 3.1-2, 3.1-1, 3.1-0, 3.0-1, 3.0-0, 2.9-1, 2.9-0

Depends bcftools

>=1.8

Depends bedtools

Depends bwa

>=0.7.17

Depends emboss

>=6.0

Depends freebayes

>=1.1

Depends minimap2

>=2.10

Depends parallel

>=20170422

Depends perl

Depends perl-bioperl

>=1.7.2

Depends perl-time-piece

Depends samclip

>=0.2

Depends samtools

>=1.8

Depends seqtk

>=1.2

Depends snp-sites

>=2.4

Depends snpeff

>=4.3

Depends vcflib

Depends vt

>=0.5772

Requirements

Installation

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

conda install snippy

and update with:

conda update snippy

or use the docker container:

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

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