• Running Trinity
• Typical Trinity Command Line
• Options to Consider when Running Trinity
• Quality trimming using Trimmomatic
• Assembling Large RNA-Seq Data Sets (hundreds of millions to billions of reads)
• Minimizing Falsely Fused Transcripts Derived from Gene Dense Genomes (using --jaccard_clip)
• [OPTIONAL] Adapting Trinity to a computing grid for massively parallel processing of embarrassingly parallel steps
• Running Trinity in multiple sequential stages