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Tomato 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 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 

on your job folder at HCI-servers. While simplifying most of the works for general users, Tomato 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.

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

Bugs? Feature requests? Add an artifact to the USeq trackers . It's best if you register and login to SourceForge so we can contact you with follow up questions.

Guide for General User

Guide for Pipeline Builder

Tomato Manual