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As of April 2, 2015 Tomato has been retired, and is no longer running. Please use the new Pysano service instead.

Note: TomatoFarmer is fully compatible with Pysano.

Tomato2 is the new version of Tomato which supported many new features including fully customizable pipelines and versioned pipelines.

Tomato2 is a computing and management framework for Next Generation Sequencing Data Analysis, running on high performance computing clusters. Basically, it works like a proxy which will accept your job request, assigned it to appropriate internal pipeline and execute the pipeline on back-end computational cluster nodes and return all results back to you. Tomato, you can do complex NGS data analysis easily.

The main features of Tomato2 are:


Tomato was designed to simplify all the steps to do high-throughput sequencing data analysis and greatly reduce your workload to do so. Most of your jobs can be done with single line of meta-command like

@align -g hg19 -i *.txt.gz


With version, Analysis results are guaranteed to be replicable, no matter how we change/update the backend bioinformatics applications and library files.


While Tomato simplifies most of the works for general users, it also keeps the full capability for expert users. You can customize most of the parameters passed to individual applications that were used in Tomato to meet special needs. In addition to pre-defined pipeline, you can easily build you own NGS data analysis pipelines by combining components.


Tomato2 is 24*7 service, processing jobs with our 14-node cluster computer on parallel.

To use Tomato, you'll need an account on the hci-moab linux server (request one via CATG). Run through the Demos below. A bit rusty on command line programming? Work through the 1hr Unix tutorial.

Questions? Comment? Search the tomato_users list and or send it an email ( ). For regular users join the list by sending an email to with the Subject line : Subscribe tomato_users YourFirstName YourLastName

Guide for General User

Guide for Pipeline Builder

Tomato Manual