recipe shovill-se

An fork of Shovill (microbial assembly pipeline for Illumina paired-end reads) that supports single-end reads.

Homepage:

https://github.com/rpetit3/shovill

License:

GPL2

Recipe:

/shovill-se/meta.yaml

package shovill-se

Versions:

1.1.0se-2,  1.1.0se-1,  1.1.0se-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:

• bactopia-assembler

Installation

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

conda install shovill-se

and update with:

conda update shovill-se

or use the docker container:

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

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

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Link to this page

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