I am a research assistant and part of a small group at UT Austin that helps biologists with bioinformatics questions. I do a fair number of transcriptome assemblies, and am very interested in some newer assemblers that take read depth into account, like Shannon and BinPacker.
To do assemblies I use TACC, our local HPC cluster. We have a few 1TB RAM largemem nodes, and thousands of compute nodes. However, there is also a 48-hour time limit on jobs that run on these nodes.
My question: does Shannon include breakpoints like Trinity that would allow me to run sequential steps as separate jobs on the cluster? I'd be particularly interested in being able to run the RAM-intensive steps on the largemem nodes, and the parallelizable steps on several normal compute nodes. It's particularly important that I be able to run the individual steps within the 48-hour time limit for individual jobs.
Shannon looks like a very interesting project, hope y'all keep up development! Thanks,
Benni Goetz
Bioinformatics Consulting Group
Center for Computational Biology and Bioinformtics
University of Texas at Austin
I am a research assistant and part of a small group at UT Austin that helps biologists with bioinformatics questions. I do a fair number of transcriptome assemblies, and am very interested in some newer assemblers that take read depth into account, like Shannon and BinPacker.
To do assemblies I use TACC, our local HPC cluster. We have a few 1TB RAM largemem nodes, and thousands of compute nodes. However, there is also a 48-hour time limit on jobs that run on these nodes.
My question: does Shannon include breakpoints like Trinity that would allow me to run sequential steps as separate jobs on the cluster? I'd be particularly interested in being able to run the RAM-intensive steps on the largemem nodes, and the parallelizable steps on several normal compute nodes. It's particularly important that I be able to run the individual steps within the 48-hour time limit for individual jobs.
Shannon looks like a very interesting project, hope y'all keep up development! Thanks,
Benni Goetz Bioinformatics Consulting Group Center for Computational Biology and Bioinformtics University of Texas at Austin