Accessing Trinity on Publicly Available Compute Resources
Brian Haas edited this page Jun 1, 2018
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6 revisions
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Point-and-click web-based access to running Trinity:
- Use the Trinity NCGAS Galaxy portal at https://galaxy.ncgas-trinity.indiana.edu/.
- Trinity is available at https://usegalaxy.org/, which sends jobs to PSC's new system Bridges featuring 42 3TB nodes and 4 12TB nodes (along with ~800 regular nodes).
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Unix command-line interface to running Trinity:
- Trinity is available to run directly on the large memory nodes of the Bridges system at the Pittsburgh Supercomputing Center.
- Trinity Wiki Home
- Installing Trinity
- Running Trinity
- Trinity process and resource monitoring
- Output of Trinity Assembly
- Assembly Quality Assessment
- Downstream Analyses
- Miscellaneous additional functionality that may be of interest
- Contributing code
- Trinity Tidbits
- Frequently Asked Questions (FAQ)
- There are too many transcripts! What do I do?
- How to minimize RAM usage
- How do I use reads I downloaded from SRA
- How do I identify the specific reads that were incorporated into the transcript assemblies?
- How can I perform cross-species analysis?
- How do I combine PE and SE reads?
- How can I run this in parallel on a computing grid?
- Computing and Time requirements
- Errors during Trinity run
- Killing Trinity
- Contact us