BeanSprout is a cross-platform command-line utility to load Illumina's Genotyping module and thus make some of BeadStudio's functionality available in a display-less non-windows server environment (such as a Linux/Solaris/MacOS X-based computing grid). It also works on MS Windows.

The Bonsai plug-in is an Illumina BeadStudio plug-in to generate custom report in the WTCCC signal format. This file format is also known otherwise as:

• output format of CelQuantileNorm
• one of the file formats readable by snpMatrix
• the input format of Chiamo

CelQuantileNorm - a suite of programs for preparing Affymetrix data for genotype calling with Chiamo.

snpMatrix - R package for large-scale SNP association studies

RFlowJo - R package of misc useful routines for TreeStar FlowJo users in flowcytometry

Here is a screenshot for the Bonsai plug-in:

BeanSprout 2.1 is to offer the full SNP summary table (HWE, etc), the full sample summary table (QC, missingness, etc), and part of the genotype table (XRaw/YRaw). That's 2-point-something tables, in fitting with v2.1 of Bonsai.

BeanSprout 3.0 gets hooked up to Bonsai 3.0.

The rest of the Illumina genotype table is not stored on disc files but generated on-the-fly when BeadStudio starts up, performing the Illumina affine transform normalization then the last stage of GenTrain/GenCall every time. Since Bonsai requires the affine transform, if/when BeanSprout hooks up with Bonsai, we would be nearly able to run GenTrain/GenCall on non-windows systems.

A newer CelQuantileNorm for the Affymetrix 5.0/6.0 chips is to happen at some undetermined time after BeanSprout 2.1.

Hin-Tak Leung, last updated 2008-06-09