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, usegalaxy-eu: snippy

package snippy

Versions:

4.6.0-2,  4.6.0-1,  4.6.0-0,  4.5.1-0,  4.5.0-0,  4.4.5-1,  4.4.5-0,  4.4.3-1,  4.4.3-0, 

4.6.0-2,  4.6.0-1,  4.6.0-0,  4.5.1-0,  4.5.0-0,  4.4.5-1,  4.4.5-0,  4.4.3-1,  4.4.3-0,  4.4.1-0,  4.4.0-2,  4.4.0-1,  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:

• any2fasta >=0.4

• bcftools >=1.10

• bedtools >=2.28.0

• bwa >=0.7.17

• freebayes >=1.3.1

• minimap2 >=2.17

• openjdk >=11

• parallel >=20170422

• perl

• perl-bioperl >=1.7.2

• samclip >=0.4

• samtools >=1.10

• seqtk >=1.3

• snp-sites >=2.4

• snpeff >=4.3

• vcflib >=1.0.0_rc3

• vt >=0.5772

Required By:

• bohra

• snpiphy

• bactopia-variants

• agrvate

• pathogist

• nullarbor

• pgcgap

Installation

With an activated Bioconda channel (see 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>)

Download stats

Link to this page

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