recipe shovill

Microbial assembly pipeline for Illumina paired-end reads

Homepage

https://github.com/tseemann/shovill

License

GPL2

Recipe

/shovill/meta.yaml

package shovill

Versions

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

• lighter >=1.1

• mash >=2.1

• megahit >=1.2.7

• perl

• perl-file-spec

• perl-findbin

• pigz

• pilon >=1.22

• samclip >=0.2

• samtools >=1.8

• seqtk >=1.3

• skesa >=2.2

• spades >=3.6

• trimmomatic >=0.36

• velvet >=1.2.10

Required By

• bohra

• nullarbor

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>)

Link to this page

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