recipe shovill

Microbial assembly pipeline for Illumina paired-end reads

Homepage

https://github.com/tseemann/shovill

License

GPL2

Recipe

/shovill/meta.yaml

package shovill

(downloads) docker_shovill

Versions

1.0.4-0, 1.0.1-0, 1.0.0-0, 0.9.0-1, 0.9.0-0, 0.8.0-0, 0.7.1-2, 0.7.1-1, 0.7.1-0

Depends bwa

>=0.7.17

Depends flash

>=1.2

Depends lighter

>=1.1

Depends mash

>=2.1

Depends megahit

>=1.1

Depends perl

Depends perl-file-spec

Depends perl-findbin

Depends pigz

Depends pilon

>=1.22

Depends samclip

>=0.2

Depends samtools

>=1.8

Depends seqtk

>=1.3

Depends skesa

>=2.2

Depends spades

>=3.6

Depends trimmomatic

>=0.36

Depends velvet

>=1.2.10

Requirements

Installation

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

conda install shovill

and update with:

conda update shovill

or use the docker container:

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

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