recipe shovill

Microbial assembly pipeline for Illumina paired-end reads

Homepage:

https://github.com/tseemann/shovill

License:

GPL2

Recipe:

/shovill/meta.yaml

Links:

biotools: shovill, usegalaxy-eu: shovill

package shovill

Versions:

1.1.0-1,  1.1.0-0,  1.0.9-0,  1.0.4-1,  1.0.4-0,  1.0.1-0,  1.0.0-0,  0.9.0-1,  0.9.0-0, 

1.1.0-1,  1.1.0-0,  1.0.9-0,  1.0.4-1,  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

• flash >=1.2

• kmc >=3.1

• lighter >=1.1

• megahit >=1.2.7

• perl

• perl-file-spec

• perl-findbin

• pigz

• pilon >=1.22

• samclip >=0.4

• samtools >=1.10

• seqtk >=1.3

• skesa >=2.2

• spades >=3.14

• trimmomatic >=0.36

• velvet >=1.2.10

Required By:

• chewiesnake

• aquamis

• bohra

• nullarbor

Installation

With an activated Bioconda channel (see 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>)

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