recipe vsnp3

Rapidly call, validate, and compare SNPs from FASTQ files in a timely manner utilizing large data sets.

Homepage:

https://github.com/USDA-VS/vsnp3

License:

GPL3

Recipe:

/vsnp3/meta.yaml

package vsnp3

Versions:

3.14-0,  3.13-0,  3.12-0,  3.11-0,  3.10-0,  3.09-0,  3.08-0,  3.07-0,  3.06-0, 

3.14-0,  3.13-0,  3.12-0,  3.11-0,  3.10-0,  3.09-0,  3.08-0,  3.07-0,  3.06-0,  3.05-0,  3.04-0,  3.02-0,  3.01-0

Depends:

• bcftools

• biopython >=1.79

• bwa

• cairosvg >=2.5.2

• dask >=2022.01.1

• freebayes >=1.3.5

• humanize >=3.14.0

• minimap2 >=2.24

• numpy >=1.21,<=1.23

• openpyxl >=3.0.9

• pandas >=1.4.0,<2.0

• parallel

• pigz

• py-cpuinfo

• python >=3.7

• pyvcf

• raxml >=8.2.12

• regex >=2.5.110

• samtools >=1.14

• scikit-allel >=1.3.5

• seqkit >=2.1.0

• sourmash >=4.2.4

• spades >=3.15.2

• svgwrite >=1.4.1

• vcflib

• vcftools

• xlsxwriter >=3.0.2

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install vsnp3

and update with:

conda update vsnp3

or use the docker container:

docker pull quay.io/biocontainers/vsnp3:<tag>

(see vsnp3/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/vsnp3/README.html)