GMS Conceptually Related Resources


1	Name	Published? (citation URL)	Project website (URL)	Source code available? (URL)	Commercial product? or Non-commercial	Open source	Software licenses	User must install dependencies invidually?	Cloud ready?	Cloud only?	Workflow manager included?	Job scheduler included?	Data and analysis tracking/ provenance?	Pipeline: germline?	Pipeline: somatic?	Pipeline: rna-seq exp?	Pipeline: rna-seq DE?	Pipeline: clinical?	Feature count	Comments

2	Genome Modeling System (GMS)	Pending	GMS	GMS on GitHub	Non-commercial	Yes	GNU LGPLv3	No	Yes	No	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	15	For more details on the features and advantages of the GMS, refer to the GMS manuscript.
3	Galaxy	Yes	Galaxy	Galaxy on BitBucket	Non-commercial	Yes	Academic Free License version 3.0	No	Yes	No	Yes	Yes	Yes	Yes	Yes	Yes	Yes	No	14	Not sure if shortcutting pre-existing results is a feature.
4	bcbio-nextgen	No	bcbio-nextgen	bcbio on GitHub	Non-commercial	Yes	MIT License	No	Yes	No	Yes	Yes	No	Yes	Yes	Yes	Yes	Yes	13	Similar ideas to the GMS. The pipelines are still being worked out.
5	Omics Pipe	Yes (preprint)	Omics Pipe	OmicsPipe on BitBucket	Non-commercial	Yes	MIT License	No	Yes	No	Yes	No	No	Yes	Yes	Yes	Yes	N/A	12	Similar to the GMS. The configuration settings are provided in YAML files, cluster needs to be installed separately.
6	GenePattern	Yes	GenePattern	Yes (upon email.)	Non-commercial	Yes	Custom	No	Yes	No	Yes	Yes	Yes	Yes	N/A	Yes	N/A	N/A	12	There are a lot of user-defined pipelines, some of the missing pipelines might be in them but its a little hard to find. There are other genomic pipelines for eg. Methylation etc which we have not evaluated in this comparison.
7	Illumina BaseSpace	No	Illumina BaseSpace	No	Commercial	No	Custom	No	Yes	No	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	11	Commercial solution. Not sure about flexibility to modify the sytem. Not open source.
8	BINA Genomic Analysis System	No	BINA	No	Commercial	No	Custom	No	Yes	No	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	11	The BINA platform is provided on custom hardware as an appliance you install at your institute
9	SeqWare	Yes	SeqWare	SeqWare	Non-commercial	Yes	GNU GPLv3	No	Yes	No	Yes	Yes	Yes	No	No	No	No	N/A	10	Infrastructure for analysis but doesn't have any information on analysis tools/pipelines.
10	DNA Nexus Platform	No	DNA Nexus Platform	SDK on GitHub	Commercial	Partial	Custom	No	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	No	Yes	10	DNA Nexus assumes that binary code will execute on Ubuntu 12.04/14.04. You can install and run the client and SDK on more systems but what you build must run on these flavors of Ubuntu.
11	gkno	No	gkno	gkno on GitHub	Non-commercial	Yes	MIT License	No	Yes	No	Yes	Yes	No	Yes	No	No	No	No	9	Limited number of analysis pipelines available currently.
12	NGSANE	Yes	NGSANE	NGSANE on GitHub	Non-commercial	Yes	BSD3	Yes	Yes	No	No	Yes	No	Yes	No	Yes	No	No	9	Limited number of analysis pipelines available currently. As far as we can tell no database, analysis provenance, no shortcutting, etc.
13	Appistry's Ayrris	No	Ayrris	No	Commercial	No	Custom	No	Yes	No	Yes	Yes	No	Yes	Yes	No	No	Yes	8	The company product link for Ayrris links to a blog post describing what sounds like a job scheduler? Not clear what Ayrris actually is...
14	GATK's Queue	No	GATK-Queue	GATK on GitHub	Both	Partial	MIT License & Broad Institute License	No	No	N/A	Yes	Yes	No	Yes	Yes	No	No	Yes	7	GATK is free for academic researchers but a paid license is required for commercial users. Little information on RNASeq workflows using GATK.
15	Curoverse's Arvados	No	Arvados	Arvados on GitHub	Both	Yes	Apache License - Version 2	Yes	Yes	No	Yes	No	Yes	Yes	No	No	No	No	7	Arvados has very little information on its analysis pipelines. Each prerequisite needs to be installed separately. Eight different install steps.
16	CGA's Firehose	No	CGA Firehose	No	Non-commercial	No	N/A	N/A	N/A	No	Yes	Yes	Yes	N/A	Yes	Yes	No	N/A	7	The site lets you download an executable but no source-code is available. Looks like a TCGA specific tool, no examples of usage outside the TCGA project.
17	Seven Bridges Genomics	No	SBG	No	Commercial	No	Custom	No	Yes	No	N/A	N/A	Yes	Yes	No	Yes	Yes	N/A	7	Commercial solution, not a lot of detail about the various pipelines.
18	MIT STAR	Yes	STAR	StarCluster on GitHub	Non-commercial	Yes	GNU GPLv3	Yes	Yes	Yes	Yes	Yes	No	No	No	No	No	No	3	This is an open-source cluster manager for Amazon EC2. All the infrastructure for genome analysis still needs to be built around this. Not clear if portable to other cluster environments.
19	GenomOncology	No	GenomOncology	No	Commercial	No	Custom	No	No	No	No	No	No	No	No	No	No	Yes	3	GenomeOncology's Clinical Workbench creates a clinical report based on variants that have already been called using other infrastructure. Aims to provide the last piece of the puzzle.
20	ga4gh	No	ga4gh	GA4GH on GitHub	Both	Yes	Apache License - Version 2	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	2	This project is still in very early stages. Lots of discussion on schemas/formats/ideas right now but no actual tools out yet.
21	IBM's PowerGene Orchestrator	No	PowerGene Orchestrator	No	Commercial	No	Custom	N/A	N/A	N/A	Yes	Yes	N/A	N/A	N/A	N/A	N/A	N/A	2	The online presence for this resource appears to be various blog posts. No obvious project page, source code, downloadable trials, etc. A.K.A IBM Genomic Medicine Reference Architecture
22
23	General tools that could be used as components of a genomics analysis platform.
24	Anduril. A generic workflow management system.	Yes	Anduril
25	bioKepler. A bioinformatics workflow management module for Kepler.	Yes	bioKepler
26	Bio WMS. A generic workflow management system.	Yes	BioWMS
27	BPipe. A generic tool for running and managing bioinformatics pipelines.	Yes	BPipe
28	DiscoveryNet. A generic workflow management system.	Yes	Discovery Net
29	Ergatis. A web-based utility that is used to create, run, and monitor reusable computational analysis pipelines.	Yes	Ergatis
30	KNIME. A generic development platform.	Yes	KNIME
31	Pegasus. A generic workflow management system.	Yes	Pegasus
32	Pegasys. A generic worfklow management system.	Yes	Pegasys
33	Pipeline Pilot. A generic workflow management system.	No	PipelinePilot
34	Ptero. A generic workflow manager.	No	Ptero
35	SnakeMake. A generic workflow management system.	Yes	SnakeMake
36	Tavaxy. A generic workflow management system.	Yes	Tavaxy
37	Taverna. A generic workflow management system.	Yes	Taverna
38	Triana. A generic workflow management system.	Yes	Triana
39
40
41	Genomics platforms used outside human genetics.
42	CloVR. A virtual machine instance for microbial sequence analysis and metagenomics pipelines.	Yes	CloVR
43	Bioclipse. A generic development platform.	Yes	Bioclipse
44	Synapse. A generic analysis platform.	No	Synapse
45
46	Desired feature available
47	Desired feature NOT available
48	Desired feature partially available or N/A
49	This document is in no-way complete/comprehensive and is being revised when new information is available. If you would like to submit an update, please open an issue here - https://github.com/genome/gms/issues