The Trinity software is used to build transcripts by de novo assembly of RNA-Seq reads from NextGen sequence data. The package is a complex integration of three stages: inchworm, chrysalis, and butterfly. To run this efficiently on Odyssey, these three stages should be broken in to three parts:

inchworm + chrysalis, which are RAM bound
butterfly, which is processor bound

Using a SLURM job dependency and the --gridconf option in Trinity, you can submit your assembly to Odyssey to run these two parts sequentially, using the Odyssey resources most efficiently. Please see pages 41 & 42 of our Informatics tutorial on Genome/Transcript Assembly.

NOTE: only use the bigmem partition if you require more than 250 GB of RAM for the first two stages. Trinity RAM requirements are discussed here. If you require less than this, please submit to general or unrestricted.

NOTE: you can also sidestep the large RAM rquirements by performing in silico digital normalization of your input FASTQ files, as documented on the Trinity site and in our Informatics recipe.

Last updated: February 25, 2016 at 12:10 pm

CC BY-NC 4.0 This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. Permissions beyond the scope of this license may be available at Attribution.