minimize_RAM_usage

Minimize RAM usage by Trinity

If you have a large data set (hundreds of millions of reads), and need to reduce RAM usage, include the following parameters:

  --min_kmer_cov 2 --no_parallel_norm_stats --max_memory 50G

and if you have multiple sets of fastq files (and ideally using the --samples_file parameter to specify them), try also adding the parameter:

  --normalize_by_read_set

so it'll perform the initial in silico normalization step on each pair of fastq files separately rather than combining them all into one large read set.

if submitting a job to a computing grid, continue to set the max memory allocation to ~200G if possible, but leave the above parameters as is.