recipe consensusfixer

Computes a consensus sequence with wobbles, ambiguous bases, and in-frame insertions, from a NGS read alignment.

Homepage

https://github.com/cbg-ethz/ConsensusFixer

License

GPL / GPL-3.0

Recipe

/consensusfixer/meta.yaml

package consensusfixer

(downloads) docker_consensusfixer

Versions

0.4-20.4-00.3.1-0

Depends
Required By

Installation

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

conda install consensusfixer

and update with:

conda update consensusfixer

or use the docker container:

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

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

Notes

ConsensusFixer is Java program that comes with a custom wrapper shell script. This shell wrapper is called "ConsensusFixer" and is on $PATH by default. By default "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can specify these values directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with "ConsensusFixer -Xms512m -Xmx1G"