Toolkit for experimental design and demultiplexing genotyping by sequencing experiments
GPL / GPL-3.0
Genotyping By Sequencing demultipleXing toolkit (GBSX) is a toolkit with an inline barcode demultiplexer for usage in the analysis of single read or paired-end genotyping by sequence (GBS) data, a barcode generator, a barcode discovery tool, and a restriction enzyme predictor. GBSX can easily be incorperated as a preceding analysis step for already deployed SNP pipelines.
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install gbsx
and update with:
conda update gbsx
or use the docker container:
docker pull quay.io/biocontainers/gbsx:<tag>
(see gbsx/tags for valid values for
GBSX is a Java program that comes with a custom wrapper shell script. This shell wrapper is called "gbsx" 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 "gbsx -Xms512m -Xmx1g"