recipe abyss

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

Homepage:

http://www.bcgsc.ca/platform/bioinfo/software/abyss

Documentation:

https://github.com/bcgsc/abyss#readme

Developer docs:

https://github.com/bcgsc/abyss

License:

GPL-3.0-only

Recipe:

/abyss/meta.yaml

Links:

biotools: abyss, doi: 10.1101/gr.214346.116, doi: 10.1101/gr.089532.108

package abyss

Versions:

2.3.5-0,  2.3.4-1,  2.3.4-0,  2.3.3-1,  2.3.3-0,  2.3.2-0,  2.3.1-0,  2.3.0-0,  2.2.5-1, 

2.3.5-0,  2.3.4-1,  2.3.4-0,  2.3.3-1,  2.3.3-0,  2.3.2-0,  2.3.1-0,  2.3.0-0,  2.2.5-1,  2.2.5-0,  2.2.4-0,  2.2.3-2,  2.2.3-1,  2.2.3-0,  2.2.2-0,  2.2.1-0,  2.1.5-1,  2.1.5-0,  2.1.4-0,  2.1.3-0,  2.1.1-0,  2.1.0-0,  2.0.2-5,  2.0.2-4,  2.0.2-3,  2.0.2-2,  2.0.2-1,  2.0.2-0,  2.0.1-2,  2.0.1-1,  2.0.1-0,  1.9.0-7,  1.9.0-6,  1.9.0-5,  1.9.0-4,  1.9.0-3,  1.9.0-2,  1.9.0-1,  1.9.0-0,  1.5.2-5,  1.5.2-4,  1.5.2-3,  1.5.2-2,  1.5.2-1,  1.5.2-0

Depends:

• libgcc-ng >=12

• libstdcxx-ng >=12

• make

• openmpi >=4.1.3,<5.0a0

• perl

• util-linux

Required By:

• komb

• secapr

• tritimap

• intemap

• vsnp

• bttoxin_digger

• pgcgap

• transabyss

• ntlink

• phyluce

Installation

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

conda install abyss

and update with:

conda update abyss

or use the docker container:

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

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

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