Computing and Time requirements
Patrick Douglas edited this page Apr 3, 2019
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Ideally, you will have access to a large-memory server, roughly having ~1G of RAM per 1M reads to be assembled. The memory usage mostly depends on the complexity of the RNA-Seq data set, specifically on the number of unique k-mers. If you do not have access to a high-memory server, other freely available options are available.
Trinity run-time depends on a number of factors including the number of reads to be assembled and the complexity of the transcript graphs. The assembly from start to finish can take anywhere from ~1/2 hour to 1 hour per million reads (your mileage may vary). If you have a large data set, be sure to use the --normalize_reads parameter to greatly improve run times.
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- Computing and Time requirements
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