Table 5. Comparison of GobyWeb with other NGS Analysis Systems.

System	Efficient Use of Storage capacity	HTS data assays supported	Flexibility	Automatically installs dependencies:		HTS data/General purpose system	Parallel analyses on compute grid
				software	data
Anduril [32]	++	Varied, depends on available workflows	+++++(5)	Y	Some	General purpose	N
Galaxy [24]	+(1)	RNASeq pipelines provided	+++ (6)	Y	Y	General purpose	Limited (11)
GenePattern [33]	++ (2)	Varied, depends on available workflows	+++	Some (8)	N (9)	General purpose	N (12)
GobyWeb (this report)	+++ (3)	RNA-Seq, DNA methylation, DNA-Seq	++ (7)	Y	Y	HTS data	Y (13)
MyRna [1]	++ (4)	RNA-Seq	+	Y	N	HTS data	Y (14)
Taverna [23]	++	Varied, depends on available workflows	+++ (6)	N/A	Y (10)	General purpose	Y (15)

Notes: (1) Supports text files.

(2) Supports any file format.

(3) Supports Goby compressed file formats.

(4) Supports BAM.

(5) Provides a scripting language specialized for pipeline development.

(6) Pipelines can be constructed by connecting components graphically.

(7) Pipelines are optimized for analysis of large HTS datasets.

(8) For example, installs Perl on Windows, but not on other platforms.

(9) Data often needs to be installed on execution server.

(10) Relies on remote web services.

(11) Very few file formats support parallelization.

(12) Runs analyses on a single server.

(13) All analyses are fully parallel.

(14) Deploys to Amazon AWS for Hadoop.

(15) Some extensions support execution on grid.