je-suite

downloads

Je is a suite to handle barcoded fastq files with (or without) Unique Molecule Identifiers (UMIs) and filter read duplicates using these UMIs

Home https://gbcs.embl.de/Je
Versions 1.2
License MIT License
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/je-suite

Installation

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

conda install je-suite

and update with:

conda update je-suite

Notes

Je is Java program that comes with a wrapper shell script. By default “-Xmx4G -Xms256m” 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 “je -Xms512m -Xmx1g”

docker

A Docker container is available at https://quay.io/repository/biocontainers/je-suite.